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Flagged for expert review before being relied on."}]}],"reuse":[{"publication":{"pmid":"40488620","pmcid":"PMC12409279","doi":"10.1158/2159-8290.cd-24-1488","title":"Federated Deep Learning Enables Cancer Subtyping by Proteomics.","journal":"Cancer discovery","year":2025,"authors_short":"Cai et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/40488620/","is_open_access":true,"citation_count":11,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"DATA_AVAILABILITY, METHODS","author_keys":["aguilar-mahecha a","aref a","armengol c","balleine r","barranco m","basik m","bowman e","boys e","cai z","clifton-bligh r","connolly e","cooper w","dalal b","dausmann m","defazio a","filipits m","flynn p","george j","gill a","gnant m","graham j","habib r","hains p","harris c","harvey k","horvath l","jackson c","koh j","kohonen-corish m","lim e","liu j","long g","lord r","lucas n","mackenzie k","mann g","mccaughan g","morgan l","murphy l","nagabushan s","nagrial a","navinés j","noor z","panizza b","poulos r","reddel r","robinson p","samra j","scolyer r","souglakos j","swarbrick a","thomas d","williams s","xavier d","zhong q"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DATA_AVAILABILITY:\"PDC000109\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:29:56.004559Z","snippet":null,"locator":"accession \"PDC000109\" indexed in DATA_AVAILABILITY","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. 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Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]}],"reuse_metrics":{"n_candidates_screened":3,"n_by_tier":{"t3_analyzed":3,"t2_declared":3,"t1_accession":0,"t0_mention":1},"n_by_tier_raw":{"t3_analyzed":3,"t2_declared":3,"t1_accession":0,"t0_mention":1},"accession_precision":{"token":"PDC000109","query":"METHODS:\"PDC000109\"","strategy_id":"epmc-literal-precision-v1","needs_correction":false,"precision":1.0,"precision_low":1.0,"precision_high":1.0,"n_sampled":0,"n_checked":0,"n_literal":0,"note":"This accession is a single indexed term, so Europe PMC matches it exactly and the hit count needs no correction."},"n_citations_to_primary_publication":null,"citation_to_reuse_ratio":null,"has_citable_accession":true,"n_verified_reuse":3,"n_reuse_examined":6,"n_independent_reuse":0,"n_nci_funded_reuse":1,"first_reuse_year":2024,"latest_reuse_year":2026,"years_since_release":1.72,"expected_reuse":0.12,"reuse_gap_index":1.833,"reuse_gap_percentile":89.4,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:48.930206Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search","source_label":"Europe PMC section-scoped hit counts","retrieved_at":"2026-09-20T18:07:48.930206Z","snippet":null,"locator":"tokens: PDC000109; queries: METHODS:\"PDC000109\"; DATA_AVAILABILITY:\"PDC000109\"; ACCESSION_ID:\"PDC000109\"; REF:\"PDC000109\"","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Index strategy epmc-index-v3. Every dataset is measured with the same single section field per tier, so the counts are comparable; the per-tier value is the largest across the dataset's own accessions, excluding any accession shared with other datasets in the corpus. This accession is a single indexed term, so Europe PMC matches it exactly and the hit count needs no correction."},{"method":"derived","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search","source_label":"Europe PMC first-reference dating","retrieved_at":"2026-09-20T18:16:12.121922Z","snippet":null,"locator":"first referenced in 2025 (METHODS section)","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Availability dated from the literature (epmc-first-reference-v2) rather than from repository file timestamps, which record re-harmonization. This is a lower bound on availability."}]},"underexplored":{"is_underexplored":false,"basis":["Reuse is within the expected range for comparable datasets (index +1.83)."],"index_value":1.833,"percentile":89.4,"comparator_set":"132 datasets in this corpus with a citable accession and sufficient metadata","evidence":[{"method":"derived","source_url":null,"source_label":"Reuse Gap Index (rgi-huber-v2)","retrieved_at":"2026-09-21T02:11:22.976067Z","snippet":null,"locator":"Huber robust regression of log2(analyzing articles + 1) on cohort size, years available, modality breadth and access tier","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Model, covariates and coefficients are published with the dataset export so the label can be recomputed or contested."}]},"grants":[{"core_project_num":"U01CA214194","project_num":null,"title":"Development of Protein Biomarkers in Post-DRE Urine for use in Liquid Biopsy of Prostate Cancer","pi_names":["Paul Christopher Boutros","Thomas Kislinger","OLIVER John SEMMES"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2016,2017,2018,2019,2020,2021],"award_amount_usd":2517754,"org_name":"EASTERN VIRGINIA MEDICAL SCHOOL","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA214194","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T03:29:56.116609Z","snippet":null,"locator":"PMID 42466117 reported under U01CA214194","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":"R01CA244729","project_num":null,"title":"The Evolution of Sarcoma Drug Sensitivity through Time and Space","pi_names":["Paul Christopher Boutros","Alice Soragni"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2020,2021,2022,2023,2024],"award_amount_usd":3386703,"org_name":"UNIVERSITY OF CALIFORNIA LOS ANGELES","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA244729","role":"reuse","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T03:29:56.116609Z","snippet":null,"locator":"PMID 42466117 reported under R01CA244729","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":"P30CA016042","project_num":null,"title":"Epigenomics, RNA, and Gene Regulation (ERGR)","pi_names":["Kathrin Plath","Richard S Finn","Roshan Bastani","Melissa Fitzmaurice Neligan","Beth A. 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It is not a reviewer's account of this dataset."}]},{"order":3,"action":"Resolve the study UUID, then fetch the file manifest","detail":"filesPerStudy keys on the study UUID, not on PDC000109: 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=\"PDC000109\")[\"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":"2026-09-21T12:30:59.435004Z","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/pdc-prospective-colon-vu-proteome.json","jsonld_url":"/data/jsonld/pdc-prospective-colon-vu-proteome.jsonld","croissant_url":"/data/croissant/pdc-prospective-colon-vu-proteome.json","instructions_url":"/data/agent/pdc-prospective-colon-vu-proteome.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":39.3,"tags":["pdc","proteogenomics"],"search_text":null}