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Please see the HCMI-CMDC Zenodo page to learn more about the images and to obtain any supporting metadata for this collection.","locator":"accession extracted from description prose","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Cross-repository link recovered from prose; verify before relying on it."}]}],"repository":{"name":"NCI Genomic Data Commons","short_name":"GDC","url":"https://portal.gdc.cancer.gov","is_nci_crdc_node":true,"is_nih_repository":true},"additional_repositories":[{"name":"NCI Imaging Data 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Not machine-generated."}]},{"order":3,"action":"Submit a dbGaP data access request for sequence data","detail":null,"url":"https://gdc.cancer.gov/access-data/obtaining-access-controlled-data","requires":["eRA Commons account","institutional signing official approval"],"est_time":"days to a few weeks","cli_snippet":null,"audience":"human","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908149Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"order":4,"action":"Query the project from code, with no credentials","detail":"The file index is public even where files are not, so an agent can size the cohort before anyone requests access.","url":"https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/","requires":[],"est_time":null,"cli_snippet":"curl -s 'https://api.gdc.cancer.gov/files' --get \\\n  --data-urlencode 'filters={\"op\":\"in\",\"content\":{\"field\":\"cases.project.project_id\",\"value\":[\"HCMI-CMDC\"]}}' \\\n  --data-urlencode 'fields=file_id,file_name,data_type' \\\n  --data-urlencode 'size=10000' --data-urlencode 'format=TSV'","audience":"agent","evidence":[{"method":"derived","source_url":"https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/","source_label":"GDC access documentation","retrieved_at":"2026-09-21T12:30:59.429218Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":5,"action":"Pass the token when the agent needs controlled files","detail":"Without a token, an API query may return only the open subset. Compare returned counts with the record before treating them as the whole cohort.","url":"https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/","requires":["GDC authentication token"],"est_time":null,"cli_snippet":"curl -H \"X-Auth-Token: $GDC_TOKEN\" https://api.gdc.cancer.gov/data/<file_id>","audience":"agent","evidence":[{"method":"derived","source_url":"https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/","source_label":"GDC access documentation","retrieved_at":"2026-09-21T12:30:59.429220Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]}],"analysis_examples":[{"level":"advanced","title":"Join the same patients across two NCI repositories","question":"Which cohorts have both imaging and molecular data on the same patients, and how many patients actually carry both?","problem":"Molecular and imaging data for the same cohort live in separate NCI repositories.","lesson":"Join shared patient identifiers and quantify the real multimodal overlap, not the advertised totals.","figure":"Paired horizontal bars per cohort comparing GDC molecular case counts with IDC imaging patient counts, where the shorter bar is the ceiling on a multimodal study of that cohort.","featured":true,"inputs":["Open GDC and IDC APIs, no account required","pandas"],"outputs":["Patient-level intersection between a GDC project and an IDC collection","Counts of molecular-only, imaging-only and joined patients","A map of every cohort present in both repositories","A chart comparing molecular and imaging patient counts per linkable cohort"],"steps":["Retrieve patient identifiers from the GDC project","Query IDC's public SQL endpoint for the collection's patient identifiers","Intersect on the shared barcode and quantify the overlap","Sweep every GDC project against every IDC collection"],"findings":["All 1,098 TCGA-BRCA patients appear in both the GDC and the IDC, a 100% join with nothing imaging-only.","39 cohorts exist in both repositories, covering 15,761 patients.","HCMI-CMDC holds 805 molecular cases but 382 imaging patients, so its multimodal ceiling is 382, not 805."],"contributor":null,"contributor_url":null,"language":"python","est_runtime":"about two minutes","est_compute":null,"workbook_path":"workbooks/python/05_cross_repository_linkage.py","workbook_url":null,"notebook_download_url":"/data/notebooks/05_cross_repository_linkage.ipynb","notebook_preview_url":"/data/notebooks/05_cross_repository_linkage.png","notebook_preview_width":1045,"notebook_preview_height":1045,"colab_url":null,"binder_url":null,"receipt":{"executed":true,"executed_at":"2026-09-21T00:43:01.297366Z","runtime_seconds":4.98,"executor":"nbclient / python 3.12.13 / Darwin 25.5.0 arm64","package_versions":{"python":"3.12.13","pandas":"3.0.6","numpy":"2.5.3","matplotlib":"3.11.2","lifelines":"0.30.0","scipy":"1.18.1","requests":"2.34.2","httpx":"0.28.1"},"n_cells":6,"n_cells_executed":6,"output_hash":"fe7a493665d23ae04c207c4b406923c9","data_retrieved_at":null,"error":null},"template_source":"05_cross_repository_linkage","evidence":[{"method":"curated","source_url":null,"source_label":"CD2S workbook","retrieved_at":"2026-09-21T12:30:59.450367Z","snippet":null,"locator":"workbooks/python/05_cross_repository_linkage.py","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Executed end to end against the live public APIs; the receipt records when, with which package versions and how long it took."}]}],"agent_package":{"json_url":"/data/datasets/gdc-hcmi-cmdc.json","jsonld_url":"/data/jsonld/gdc-hcmi-cmdc.jsonld","croissant_url":"/data/croissant/gdc-hcmi-cmdc.json","instructions_url":"/data/agent/gdc-hcmi-cmdc.md","bundle_url":null,"mcp_resource_uri":null},"related_dataset_ids":[],"related_underexplored_ids":[],"review":{"status":"project_curated","reviewer":"CD2S project curation","reviewer_affiliation":null,"reviewed_at":"2026-09-18","sections_reviewed":["useful_for","limitations","inappropriate_uses","access_steps"],"open_questions":[],"notes":null},"verification":{"last_verified_at":null,"link_checks":[],"n_links_ok":0,"n_links_broken":0,"upstream_version_seen":null,"upstream_version_changed":false,"upstream_counts_seen":{},"upstream_drift":{},"notes":[]},"is_showcase":true,"completeness_score":92.9,"tags":["gdc","hcmi","idc","imaging","model-systems","multi-tumor","organoids","rare-cancers","released"],"search_text":null}