Q (sonnet): download MSK-CHORD study on Non-Small Cell Lung Cancer dataset

▶ resolve_and_route
{
 "studyKeywords": [
  "MSK",
  "CHORD"
 ]
}

◀ result
{"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","sampleCount":25040,"studyViewUrl":"https://www.cbioportal.org/study?id=msk_chord_2024","metadata":{"clinicalAttributeIds":["ADRENAL_GLANDS","BONE","CANCER_TYPE","CANCER_TYPE_DETAILED","CLINICAL_GROUP","CLINICAL_SUMMARY","CNS_BRAIN","CURRENT_AGE_DEID","DIAGNOSIS_DESCRIPTION","ETHNICITY","FRACTION_GENOME_ALTERED","GENDER","GENE_PANEL","GLEASON_FIRST_REPORTED","GLEASON_HIGHEST_REPORTED","GLEASON_SAMPLE_LEVEL","HER2","HISTORY_OF_PDL1","HR","ICD_O_HISTOLOGY_DESCRIPTION","INTRA_ABDOMINAL","LIVER","LUNG","LYMPH_NODES","METASTATIC_SITE","MSI_COMMENT","MSI_SCORE","MSI_TYPE","MUTATION_COUNT","NUM_ICDO_DX","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER","PATHOLOGICAL_GROUP","PDL1_POSITIVE","PLEURA","PRIMARY_SITE","PRIOR_MED_TO_MSK","RACE","REPRODUCTIVE_ORGANS","SAMPLE_CLASS","SAMPLE_COUNT","SAMPLE_COVERAGE","SAMPLE_TYPE","SMOKING_PREDICTIONS_3_CLASSES","SOMATIC_STATUS","STAGE_HIGHEST_RECORDED","TMB_NONSYNONYMOUS","TUMOR_PURITY"],"molecularProfileIds":["msk_chord_2024_cna","msk_chord_2024_mutations","msk_chord_2024_structural_variants"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations"]}}]}}

▶ search_oncotree
{
 "search_term": "Non-Small Cell Lung Cancer"
}

◀ result
{"result":[{"code":"NSCLC","name":"Non-Small Cell Lung Cancer","score":80,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC"},{"code":"ALUCA","name":"Atypical Lung Carcinoid","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > LNET > ALUCA"},{"code":"BLCLC","name":"Basaloid Large Cell Carcinoma of the Lung","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LCLC > BLCLC"},{"code":"CCLC","name":"Clear Cell Carcinoma of the Lung","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LCLC > CCLC"},{"code":"CMPT","name":"Ciliated Muconodular Papillary Tumor of the Lung","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > CMPT"},{"code":"GCLC","name":"Giant Cell Carcinoma of the Lung","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LCLC > GCLC"},{"code":"IMTL","name":"Inflammatory Myofibroblastic Lung Tumor","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > IMTL"},{"code":"LAIS","name":"Lung Adenocarcinoma In Situ","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > LAIS"},{"code":"LAM","name":"Pulmonary Lymphangiomyomatosis","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > LAM"},{"code":"LCLC","name":"Large Cell Lung Carcinoma","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LCLC"},{"code":"LECLC","name":"Lymphoepithelioma-like Carcinoma of the Lung","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LCLC > LECLC"},{"code":"LNET","name":"Lung Neuroendocrine Tumor","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > LNET"},{"code":"LUACC","name":"Adenoid Cystic Carcinoma of the Lung","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > SGTTL > LUACC"},{"code":"LUAD","name":"Lung Adenocarcinoma","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LUAD"},{"code":"LUAS","name":"Lung Adenosquamous Carcinoma","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LUAS"},{"code":"LUCA","name":"Lung Carcinoid","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > LNET > LUCA"},{"code":"LUMEC","name":"Mucoepidermoid Carcinoma of the Lung","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > SGTTL > LUMEC"},{"code":"LUNE","name":"Large Cell Neuroendocrine Carcinoma","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > LNET > LUNE"},{"code":"LUPC","name":"Pleomorphic Carcinoma of the Lung","score":65,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierar … (999 more chars)

▶ get_studyviewfilter_options
{
 "studyId": "msk_chord_2024",
 "attributeIds": [
  "CANCER_TYPE"
 ]
}

◀ result
{"success":true,"message":"Successfully retrieved StudyView filter options","data":{"studyId":"msk_chord_2024","attributes":[{"attributeId":"CANCER_TYPE","displayName":"Cancer Type","description":"The main cancer type as defined by the Oncotree cancer classification system for precision oncology. Source: MPath","datatype":"STRING","values":["Non-Small Cell Lung Cancer","Colorectal Cancer","Prostate Cancer","Pancreatic Cancer","Breast Cancer"]}]}}

▶ navigate_to_study_view
{
 "studyIds": [
  "msk_chord_2024"
 ],
 "filterJson": {
  "clinicalDataFilters": [
   {
    "attributeId": "CANCER_TYPE",
    "values": [
     {
      "value": "Non-Small Cell Lung Cancer"
     }
    ]
   }
  ]
 }
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/study/summary?id=msk_chord_2024#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Non-Small%20Cell%20Lung%20Cancer%22%7D%5D%7D%5D%7D","url":"https://www.cbioportal.org/study/summary?id=msk_chord_2024#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Non-Small%20Cell%20Lung%20Cancer%22%7D%5D%7D%5D%7D","data":{"studyIds":["msk_chord_2024"],"studies":[{"studyId":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","sampleCount":25040}],"tab":"summary","hasFilters":true,"hasPlotsConfig":false,"pageDescription":"Overview of all study data displayed as interactive charts summarizing available clinical and genomic data. Click within a chart to filter. Additional charts may be available in the Charts menu."}}

═ answer (success)
Here's the link to the NSCLC subset of the **[MSK-CHORD (MSK, Nature 2024)](https://www.cbioportal.org/study/summary?id=msk_chord_2024#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Non-Small%20Cell%20Lung%20Cancer%22%7D%5D%7D%5D%7D)** study:

- **Full study:** 25,040 samples across five cancer types (NSCLC, colorectal, prostate, pancreatic, breast).
- The link above is pre-filtered to samples where Cancer Type = "Non-Small Cell Lung Cancer" — the study overview page will show you the exact filtered sample/patient count once loaded.

**To download the data:**
1. Open the link above.
2. Once the NSCLC filter is applied, click **"Add Charts" is not needed** — instead use the checkbox/selection tool at the top of the sample table to select the filtered cohort, or simply use the **Download** icon (⬇) in the top right of the summary page.
3. This lets you export clinical data (TSV) directly. For full genomic data (mutations, CNA, structural variants) bundled together, use the **"Download"** tab option on the study page, or query the public API endpoint:
   `https://www.cbioportal.org/api/studies/msk_chord_2024/clinical-data` (and similarly `/mutations`, `/copy-number-seg`, etc.), filtering client-side to NSCLC samples.

Note: NSCLC in this cohort spans multiple histologies (adenocarcinoma, squamous cell, etc.) — if you want a narrower subtype (e.g., only LUAD), let me know and I can refine the filter further.