Q (haiku): is there any imaging data?

▶ 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": "resource_definition"
}

▶ clickhouse_list_table_columns
{
 "table": "resource_study"
}

◀ result
{"columns":[{"name":"resource_id","type":"String"},{"name":"display_name","type":"String"},{"name":"description","type":"Nullable(String)"},{"name":"resource_type","type":"String"},{"name":"open_by_default","type":"Nullable(Int32)"},{"name":"priority","type":"Int64"},{"name":"cancer_study_id","type":"Int64"},{"name":"custom_metadata","type":"Nullable(String)"}]}

▶ clickhouse_list_table_columns
{
 "table": "resource_patient"
}

◀ result
{"columns":[{"name":"internal_id","type":"Int64"},{"name":"resource_id","type":"String"},{"name":"url","type":"String"}]}

▶ clickhouse_list_table_columns
{
 "table": "resource_sample"
}

◀ result
{"columns":[{"name":"internal_id","type":"Int64"},{"name":"resource_id","type":"String"},{"name":"url","type":"String"}]}

◀ result
{"columns":[{"name":"internal_id","type":"Int64"},{"name":"resource_id","type":"String"},{"name":"url","type":"String"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT resource_type
FROM resource_definition
ORDER BY resource_type
",
 "max_rows": 50
}

◀ result
{"rows":[{"resource_type":"PATIENT"},{"resource_type":"SAMPLE"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT resource_type, COUNT(*) as count
FROM resource_definition
GROUP BY resource_type
ORDER BY count DESC
",
 "max_rows": 50
}

◀ result
{"rows":[{"resource_type":"PATIENT","count":74},{"resource_type":"SAMPLE","count":10}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
  resource_id,
  display_name,
  description,
  resource_type,
  cancer_study_id
FROM resource_definition
ORDER BY resource_type, display_name
LIMIT 30
",
 "max_rows": 100
}

◀ result
{"rows":[{"resource_id":"IDC_OHIF_CR","display_name":"Computed Radiography","description":"Computed Radiography","resource_type":"PATIENT","cancer_study_id":749},{"resource_id":"IDC_OHIF_CR","display_name":"Computed Radiography","description":"Computed Radiography","resource_type":"PATIENT","cancer_study_id":763},{"resource_id":"IDC_OHIF_CR","display_name":"Computed Radiography","description":"Computed Radiography","resource_type":"PATIENT","cancer_study_id":787},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":735},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":736},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":737},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":739},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":742},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":743},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":745},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":747},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":749},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":756},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":759},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":763},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":764},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":768},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","cancer_study_id":787},{"resource_id":"IDC_OHIF_DX","display_name":"Digital Radiography","description":"Digital Radiography","resource_type":"PATIENT","cancer_study_id":787},{"resource_id":"FIGURES","display_name":"Figures","description":"Figures from https://www.biorxiv.org/content/10.110 … (1563 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
  display_name,
  COUNT(*) as num_studies
FROM resource_definition
WHERE resource_type = 'PATIENT'
GROUP BY display_name
ORDER BY num_studies DESC
",
 "max_rows": 50
}

◀ result
{"rows":[{"display_name":"Slide Microscopy","num_studies":31},{"display_name":"Computed Tomography","num_studies":15},{"display_name":"Magnetic Resonance","num_studies":11},{"display_name":"Positron Emission Tomography","num_studies":8},{"display_name":"Computed Radiography","num_studies":3},{"display_name":"Nuclear Medicine","num_studies":2},{"display_name":"Figures","num_studies":1},{"display_name":"Mammography","num_studies":1},{"display_name":"MxIF Image","num_studies":1},{"display_name":"Digital Radiography","num_studies":1}]}

═ answer (success)
## Yes, there is imaging data available in cBioPortal

The database contains **patient-level imaging resources** linked through the **IDC (Imaging Data Commons)** and OHIF (Open Health Imaging Foundation) viewer. Here's what's available:

### Imaging Modalities (by number of studies):
- **Slide Microscopy** — 31 studies
- **Computed Tomography (CT)** — 15 studies
- **Magnetic Resonance (MRI)** — 11 studies
- **Positron Emission Tomography (PET)** — 8 studies
- **Computed Radiography** — 3 studies
- **Nuclear Medicine** — 2 studies
- **Mammography** — 1 study
- **MxIF Image** (Multiplexed Immunofluorescence) — 1 study
- **Digital Radiography** — 1 study

### How to Access
When viewing a patient profile in cBioPortal (PatientView), if imaging data is available for that patient, you'll see a clickable link under the corresponding imaging modality (e.g., "Computed Tomography"). These links launch the **OHIF viewer**, which allows interactive exploration of medical images from the Imaging Data Commons.

### Sample-Level Resources
In addition to patient-level imaging (74 resources), there are also **10 sample-level resources** available for specific tissue samples.

Would you like me to identify which studies have imaging data, or navigate you to a specific study with imaging available?