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the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U24CA271114","project_num":null,"title":"Proteogenomic translator for cancer biomarker discovery towards precision medicine","pi_names":["Avi Ma'ayan","Pei Wang"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":5022764,"org_name":"ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA271114","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:53.697446Z","snippet":null,"locator":"PMID 40749670 reported under U24CA271114","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream 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Guccione","Matthew Galsky","Therica Miller","DEBORAH DOROSHOW","Julio A. Aguirre-Ghiso","MARSHALL R POSNER","KEVIN A KELLEY","Nina A. Bickell","Cardinale B Smith","MYRON E SCHWARTZ","SCOTT L. FRIEDMAN","Steven J. Burakoff","Paolo Boffetta","VICTOR Louis FRIEDRICH"],"agency_ic":"NCI","activity_code":"P30","fiscal_years":[2015,2016,2017,2018,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":63610997,"org_name":"ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P30CA196521","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:53.697446Z","snippet":null,"locator":"PMID 40749670 reported under P30CA196521","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U19CA203654","project_num":null,"title":"Integrative Analysis of Lung Cancer Etiology and Risk","pi_names":["Christopher I. Amos","Rayjean J. Hung","Mattias Alexander Johansson","XIHONG LIN","Paul Joseph Brennan"],"agency_ic":"NCI","activity_code":"U19","fiscal_years":[2017,2018,2019,2020,2021,2022,2023,2024,2026],"award_amount_usd":41984890,"org_name":"UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U19CA203654","role":"reuse","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:53.697446Z","snippet":null,"locator":"PMID 34002017 reported under U19CA203654","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U01CA209414","project_num":null,"title":"The Boston Lung Cancer Survival Cohort","pi_names":["David C Christiani"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2017,2018,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":12210984,"org_name":"HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA209414","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:53.697446Z","snippet":null,"locator":"PMID 34002017 reported under U01CA209414","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U01CA167462","project_num":null,"title":"Infrastructure Support and Pilot Tissue Collection for the CARET Biorepository","pi_names":["Marian L Neuhouser","CHU CHEN"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2018,2019,2020,2021,2022],"award_amount_usd":2890039,"org_name":"FRED HUTCHINSON CANCER CENTER","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA167462","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:53.697446Z","snippet":null,"locator":"PMID 34002017 reported under U01CA167462","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U01CA063673","project_num":null,"title":"THE CAROTENE AND RETINOL EFFICACY TRIAL (CARET)","pi_names":["GARY E GOODMAN","GILBERT S OMENN"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[1994,1995,1996,1997,1998,1999,2000,2001,2002,2003,2004,2005,2006],"award_amount_usd":36509786,"org_name":"FRED HUTCHINSON CANCER RESEARCH CENTER","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA063673","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:53.697446Z","snippet":null,"locator":"PMID 34002017 reported under U01CA063673","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"R01CA092824","project_num":null,"title":"Molecular and Genetic Analysis of Lung Cancer Survival","pi_names":["David C Christiani"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2002,2003,2004,2005,2007,2009,2010,2011,2012,2013],"award_amount_usd":5903917,"org_name":"HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA092824","role":"reuse","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:53.697446Z","snippet":null,"locator":"PMID 34002017 reported under R01CA092824","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]}],"access_steps":[{"order":1,"action":"Download the fractions from the PDC portal","detail":"Open access, no account required.","url":"https://pdc.cancer.gov/pdc/browse","requires":[],"est_time":"1 hour","cli_snippet":null,"audience":"human","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908986Z","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":2,"action":"Join clinical data from the GDC CPTAC-3 record","detail":null,"url":"https://portal.gdc.cancer.gov/projects/CPTAC-3","requires":[],"est_time":"2-3 hours","cli_snippet":null,"audience":"human","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908986Z","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":3,"action":"Resolve the study UUID, then fetch the file manifest","detail":"filesPerStudy keys on the study UUID, not on PDC000224: called with the pdc_study_id it returns the right number of rows with every column null. Resolve the UUID first and pass the terms acknowledgement.","url":"https://pdc.cancer.gov/data-dictionary/publicapi-documentation/","requires":[],"est_time":null,"cli_snippet":"python - <<'PY'\nimport requests\nAPI = \"https://proteomic.datacommons.cancer.gov/graphql\"\n\ndef gql(query, **variables):\n    r = requests.post(API, json={\"query\": query, \"variables\": variables}, timeout=180)\n    r.raise_for_status()\n    body = r.json()\n    if body.get(\"errors\"):\n        raise RuntimeError(body[\"errors\"][0][\"message\"])\n    return body[\"data\"]\n\nstudy = gql('query($id:String!){ study(pdc_study_id:$id acceptDUA:true){ study_id } }',\n            id=\"PDC000224\")[\"study\"][0]\nfiles = gql('query($sid:String!){ filesPerStudy(study_id:$sid acceptDUA:true)'\n            '{ file_id file_name file_size } }', sid=study[\"study_id\"])[\"filesPerStudy\"]\nprint(len(files), \"files\")\nPY","audience":"agent","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/data-dictionary/publicapi-documentation/","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.434250Z","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":"intermediate","title":"Find and use the scarcest measurements in the portfolio","question":"Where can I find ubiquitylome, lipidome or metabolome data, and which cohorts carry several scarce layers on the same tumors?","problem":"Rare proteomic layers are scattered across study records and may cover different patients.","lesson":"Find genuinely scarce measurements and bound the complete-case cohort before designing the study.","figure":"Horizontal bars of the case count for each measured layer in the target cohort, with a dashed line at the smallest layer marking the ceiling on any analysis needing every layer at once.","featured":false,"inputs":["Public PDC GraphQL API, no account required","pandas"],"outputs":["Scarcity ranking of every analytical fraction","Cohorts carrying two or more scarce layers","Layer overlap bounding a complete-case analysis","Citation counts demonstrating that PDC accessions are not quoted","A chart of per-layer coverage with the complete-case ceiling marked"],"steps":["Enumerate every PDC study through the public GraphQL endpoint","Rank analytical fractions by number of studies","Group per-fraction studies back into biological cohorts","Report the per-layer case counts that bound a complete-case analysis","Query Europe PMC for each accession to show citation tracing is blind here"],"findings":["Across 255 PDC studies the proteome appears 109 times, the ubiquitylome 5 and the lipidome 3.","CPTAC STAD carries five scarce layers on 193 cases, but a complete-case analysis across all seven is capped at 153.","Each of the six STAD accessions returns one article, so accession tracing is blind to proteomic reuse."],"contributor":null,"contributor_url":null,"language":"python","est_runtime":"about a minute","est_compute":null,"workbook_path":"workbooks/python/04_scarce_modality_cptac.py","workbook_url":null,"notebook_download_url":"/data/notebooks/04_scarce_modality_cptac.ipynb","notebook_preview_url":"/data/notebooks/04_scarce_modality_cptac.png","notebook_preview_width":1045,"notebook_preview_height":616,"colab_url":null,"binder_url":null,"receipt":{"executed":true,"executed_at":"2026-09-21T00:42:56.314549Z","runtime_seconds":107.84,"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":7,"n_cells_executed":7,"output_hash":"016ed4e8fdca36b1dd852eabc6e6ca96","data_retrieved_at":null,"error":null},"template_source":"04_scarce_modality_cptac","evidence":[{"method":"curated","source_url":null,"source_label":"CD2S workbook","retrieved_at":"2026-09-21T12:30:59.450340Z","snippet":null,"locator":"workbooks/python/04_scarce_modality_cptac.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/pdc-cptac-luad-discovery-study.json","jsonld_url":"/data/jsonld/pdc-cptac-luad-discovery-study.jsonld","croissant_url":"/data/croissant/pdc-cptac-luad-discovery-study.json","instructions_url":"/data/agent/pdc-cptac-luad-discovery-study.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":["acetylome","lung","open-access","pdc","proteogenomics","rare-modality","scarce-modality","ubiquitylome"],"search_text":null}