Q (sonnet-5.5): Can you find a study that I may emulate that has a data_clinical_outcomes.txt file and associated meta file to interogate

▶ list_guides
{}

▶ clickhouse_list_tables
{}

◀ result
{"result":[{"uri":"cbioportal://mutation-frequency-guide","description":"Comprehensive guide for calculating gene mutation frequencies with gene-specific profiling denominators"},{"uri":"cbioportal://clinical-data-guide","description":"Guide for querying clinical data including patient vs sample level considerations"},{"uri":"cbioportal://sample-filtering-guide","description":"Guide for filtering samples and studies in cBioPortal queries, including a subtype inside a multi-subtype study (e.g. adenoid cystic carcinoma in acc_2019: filter by ONCOTREE_CODE)"},{"uri":"cbioportal://common-pitfalls","description":"Guide to avoid common mistakes when querying cBioPortal data. If you already know which numbered pitfall applies, fetch just that section via read_guide(\"cbioportal://common-pitfalls#<number>\") (e.g. #16) instead of the full guide"},{"uri":"cbioportal://treatment-guide","description":"Guide for querying treatment/clinical event data including drug agents, timelines, and linking to genomic data"},{"uri":"cbioportal://faq-guide","description":"General cBioPortal FAQ: what cancer types, data types and studies the database has, history, how to cite, reference genome, abbreviations, GISTIC thresholds, API access, germline support"},{"uri":"cbioportal://statistical-tests-guide","description":"Statistical test selection guide — decision matrix for choosing Fisher's exact, Wilcoxon, chi-squared, t-test, ANOVA, etc. based on data type and group count"},{"uri":"cbioportal://gene-expression-guide","description":"Gene expression / copy-number / methylation analysis. Covers genetic_alteration_derived, profile_type discovery, and the gene_pair_coexpression view for Spearman correlation between two genes"},{"uri":"cbioportal://external-resources-guide","description":"Guide for finding external linked resources such as imaging, pathology, Minerva, HTAN, or other resource_* table links before declaring data unavailable"},{"uri":"cbioportal://gene-resolution-guide","description":"Guide for resolving ambiguous gene symbols, aliases, gene families, and shorthand such as CD3 before querying expression or alteration data"},{"uri":"cbioportal://study-resolution-guide","description":"Guide for resolving requested studies when list_studies finds nothing (e.g. HTAN centers such as OHSU, which appear only as atlas codes in study ids), avoiding silent substitute cohorts, and redirecting to known external cBioPortal instances when data is not in this deployment"},{"uri":"cbioportal://germline-guide","description":"Guide for querying germline variant data — storage columns, study discovery, query patterns, and somatic vs germline considerations"},{"uri":"cbioportal://study-guide/{study_id}","description":"Dynamic study-specific guide - use get_study_guide(study_id) tool to generate"}]}

◀ 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": "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 cs.cancer_study_identifier, cs.name, cs.sample_count, countIf(positionCaseInsensitive(m.attr_id,'outcome')>0 OR positionCaseInsensitive(m.display_name,'outcome')>0) AS outcome_attrs, groupArrayIf(m.attr_id, positionCaseInsensitive(m.attr_id,'outcome')>0 OR positionCaseInsensitive(m.display_name,'outcome')>0) AS attrs FROM clinical_attribute_meta m JOIN cancer_study cs ON cs.cancer_study_id = m.cancer_study_id GROUP BY cs.cancer_study_identifier, cs.name, cs.sample_count HAVING outcome_attrs>0 ORDER BY outcome_attrs DESC LIMIT 15"
}

◀ result
{"rows":[{"cancer_study_identifier":"rectal_msk_2022","name":"Rectal Cancer (MSK, Nature Medicine 2022)","sample_count":788,"outcome_attrs":3,"attrs":["LARC_CRT_OUTCOME_CASES_DFS","LARC_CRT_OUTCOME_CASES_RESPONSE","USE_IN_OUTCOME_ANALYSIS"]},{"cancer_study_identifier":"cesc_tcga","name":"Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA, Firehose Legacy)","sample_count":310,"outcome_attrs":3,"attrs":["FEDPET_OR_CT_RESULTS","LYMPH_NODES_SUPRACLAVICULAR","TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"ov_tcga_pub","name":"Ovarian Serous Cystadenocarcinoma (TCGA, Nature 2011)","sample_count":489,"outcome_attrs":1,"attrs":["PRIMARY_THERAPY_OUTCOME_SUCCESS"]},{"cancer_study_identifier":"coadread_tcga","name":"Colorectal Adenocarcinoma (TCGA, Firehose Legacy)","sample_count":640,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"prad_cpcg_2017","name":"Prostate Adenocarcinoma (CPC-GENE, Nature 2017)","sample_count":477,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"pcpg_tcga","name":"Pheochromocytoma and Paraganglioma (TCGA, Firehose Legacy)","sample_count":184,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"lusc_tcga","name":"Lung Squamous Cell Carcinoma (TCGA, Firehose Legacy)","sample_count":511,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"kich_tcga","name":"Kidney Chromophobe (TCGA, Firehose Legacy)","sample_count":113,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"blca_tcga","name":"Bladder Urothelial Carcinoma (TCGA, Firehose Legacy)","sample_count":413,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"prad_tcga","name":"Prostate Adenocarcinoma (TCGA, Firehose Legacy)","sample_count":501,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"gbm_tcga","name":"Glioblastoma Multiforme (TCGA, Firehose Legacy)","sample_count":619,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"stad_tcga","name":"Stomach Adenocarcinoma (TCGA, Firehose Legacy)","sample_count":478,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"acc_tcga","name":"Adrenocortical Carcinoma (TCGA, Firehose Legacy)","sample_count":92,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"kich_tcga_pub","name":"Kidney Chromophobe (TCGA, Cancer Cell 2014)","sample_count":66,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]},{"cancer_study_identifier":"lgg_tcga","name":"Brain Lower Grade Glioma (TCGA, Firehose Legacy)","sample_count":530,"outcome_attrs":1,"attrs":["TREATMENT_OUTCOME_FIRST_COURSE"]}]}

═ answer (success)
I can't confirm that any study has a file called `data_clinical_outcomes.txt`. The database I can query holds the loaded clinical attributes, not the original import files, so it doesn't record file names or their meta files. `data_clinical_outcomes.txt` also isn't one of cBioPortal's standard file names. The standard clinical files are `data_clinical_patient.txt` and `data_clinical_sample.txt`. Each has a meta file (`meta_clinical_patient.txt` or `meta_clinical_sample.txt`) with `data_filename` set to the data file.

The closest candidate I found is [Rectal Cancer (MSK, Nature Medicine 2022)](https://www.cbioportal.org/study/summary?id=rectal_msk_2022) (`rectal_msk_2022`, 788 samples). It's an MSK study with explicit outcome attributes:
- `LARC_CRT_OUTCOME_CASES_DFS`
- `LARC_CRT_OUTCOME_CASES_RESPONSE`
- `USE_IN_OUTCOME_ANALYSIS`

The study may have kept these in a separate outcomes file, but I can't verify that from here. The source data would show it: MSK's public datahub repository (`cBioPortal/datahub` on GitHub) has this study's folder. It's worth checking the file list there.

Other studies have a single outcome-type field, `TREATMENT_OUTCOME_FIRST_COURSE`. Examples are the TCGA Firehose Legacy studies (`gbm_tcga`, `lusc_tcga`, `blca_tcga`, `coadread_tcga`) and [CPC-GENE Prostate](https://www.cbioportal.org/study/summary?id=prad_cpcg_2017). These come from the TCGA clinical files, not a dedicated outcomes file.

If your aim is a template for a clinical outcomes file, the usual cBioPortal approach is to add outcome columns such as `OS_STATUS`, `OS_MONTHS`, `DFS_STATUS` and `DFS_MONTHS` to the patient clinical file. Its meta file is `meta_clinical_patient.txt` with `genetic_alteration_type: CLINICAL` and `datatype: PATIENT_ATTRIBUTES`. A custom name like `data_clinical_outcomes.txt` also works if the meta file's `data_filename` points to it.

If you tell me the cancer type or the outcomes you want (OS, DFS, response), I can find studies that have those fields.