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It is not a reviewer's account of this dataset."}]},{"order":2,"action":"Download the open files without an account","detail":"1,232 open-access files are marked open access. Add them to a portal cart, export a manifest, and fetch it with the GDC Data Transfer Tool.","url":"https://gdc.cancer.gov/access-data/gdc-data-transfer-tool","requires":[],"est_time":"minutes to hours, by cohort size","cli_snippet":"gdc-client download -m gdc_manifest.txt","audience":"human","evidence":[{"method":"derived","source_url":"https://gdc.cancer.gov/access-data/gdc-data-transfer-tool","source_label":"GDC access documentation","retrieved_at":"2026-09-21T12:30:59.437645Z","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":3,"action":"Request controlled access through dbGaP","detail":"1,942 controlled-access files require an approved data access request. The request starts at dbGaP, not in the portal. The relevant study is phs000178.","url":"https://gdc.cancer.gov/access-data/obtaining-access-controlled-data","requires":["eRA Commons account","institutional signing official approval","dbGaP data access request for phs000178"],"est_time":"days to a few weeks after signing official approval","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://gdc.cancer.gov/access-data/obtaining-access-controlled-data","source_label":"GDC access documentation","retrieved_at":"2026-09-21T12:30:59.437648Z","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":4,"action":"Download controlled files with your token","detail":"An approved request yields a token. The same manifest fetches nothing controlled without it.","url":"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000178","requires":["approved dbGaP request","GDC authentication token"],"est_time":null,"cli_snippet":"gdc-client download -m gdc_manifest.txt -t gdc-user-token.txt","audience":"human","evidence":[{"method":"derived","source_url":"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000178","source_label":"GDC access documentation","retrieved_at":"2026-09-21T12:30:59.437650Z","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":"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\":[\"TCGA-DLBC\"]}}' \\\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":"2026-09-21T12:30:59.437651Z","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":6,"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":"2026-09-21T12:30:59.437653Z","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":[],"agent_package":{"json_url":"/data/datasets/gdc-tcga-dlbc.json","jsonld_url":"/data/jsonld/gdc-tcga-dlbc.jsonld","croissant_url":"/data/croissant/gdc-tcga-dlbc.json","instructions_url":"/data/agent/gdc-tcga-dlbc.md","bundle_url":null,"mcp_resource_uri":null},"related_dataset_ids":[],"related_underexplored_ids":[],"review":{"status":"machine_only","reviewer":null,"reviewer_affiliation":null,"reviewed_at":null,"sections_reviewed":[],"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":false,"completeness_score":28.6,"tags":["gdc","idc","imaging","released","tcga"],"search_text":null}