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Flagged for expert review before being relied on."}]}],"reuse":[{"publication":{"pmid":"37505094","pmcid":"PMC10621272","doi":"10.1080/15548627.2023.2239633","title":"Starvation-inactivated MTOR triggers cell migration via a ULK1-SH3PXD2A/TKS5-MMP14 pathway in ovarian carcinoma.","journal":"Autophagy","year":2023,"authors_short":"Lin et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/37505094/","is_open_access":false,"citation_count":19,"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":"METHODS","author_keys":["chi l","huang h","lai c","lin c","tang y","tsai c"],"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=METHODS:\"PDC000114\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:31:44.237353Z","snippet":null,"locator":"accession \"PDC000114\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"35681563","pmcid":"PMC9179372","doi":"10.3390/cancers14112583","title":"Model Cell Lines and Tissues of Different HGSOC Subtypes Differ in Local Estrogen Biosynthesis.","journal":"Cancers","year":2022,"authors_short":"Pavlič et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/35681563/","is_open_access":true,"citation_count":17,"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":"METHODS","author_keys":["gjorgoska m","pavlič r","rižner t"],"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=METHODS:\"PDC000114\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:31:44.237353Z","snippet":null,"locator":"accession \"PDC000114\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"38918474","pmcid":"PMC11199488","doi":"10.1038/s41597-024-03536-1","title":"Machine Learning-Enhanced Extraction of Biomarkers for High-Grade Serous Ovarian Cancer from Proteomics Data.","journal":"Scientific data","year":2024,"authors_short":"De et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/38918474/","is_open_access":true,"citation_count":16,"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":"METHODS","author_keys":["alli-shaik a","gunaratne j"],"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=METHODS:\"PDC000114\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:31:44.237353Z","snippet":null,"locator":"accession \"PDC000114\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"39775839","pmcid":"PMC11702362","doi":"10.1093/gigascience/giae113","title":"Mutation impact on mRNA versus protein expression across human cancers.","journal":"GigaScience","year":2025,"authors_short":"Liu et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/39775839/","is_open_access":true,"citation_count":9,"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, SUPPL","author_keys":["elmas a","huang k","liu y"],"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:\"PDC000114\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:31:44.237353Z","snippet":null,"locator":"accession \"PDC000114\" indexed in DATA_AVAILABILITY","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"40276932","pmcid":"PMC12045569","doi":"10.1080/15476286.2025.2498203","title":"The implication of non-AUG-initiated N-terminally extended proteoforms in cancer.","journal":"RNA biology","year":2025,"authors_short":"Pancsa et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/40276932/","is_open_access":true,"citation_count":1,"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":"METHODS","author_keys":["andreev d","dean k","pancsa r"],"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=METHODS:\"PDC000114\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:31:44.237353Z","snippet":null,"locator":"accession \"PDC000114\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"41393507","pmcid":"PMC12698437","doi":"10.3389/fmolb.2025.1623062","title":"ZKSCAN3 promotes ovarian cancer cell proliferation by increasing HSPB1 expression.","journal":"Frontiers in molecular biosciences","year":2025,"authors_short":"Ke et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/41393507/","is_open_access":true,"citation_count":1,"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":"METHODS","author_keys":["fan l","song t","sun l","zhao h"],"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=METHODS:\"PDC000114\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:31:44.237353Z","snippet":null,"locator":"accession \"PDC000114\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"41466215","pmcid":"PMC12859830","doi":"10.1186/s10020-025-01413-0","title":"Harnessing m6A-regulated cholesterol biosynthesis helps impede tumor burden and stemness in high-garde serous ovarian carcinoma mesenchymal phenotype.","journal":"Molecular medicine (Cambridge, Mass.)","year":2025,"authors_short":"Narayanan et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/41466215/","is_open_access":true,"citation_count":0,"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":"METHODS","author_keys":["bapat s","dhenge k","narayanan a"],"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=METHODS:\"PDC000114\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:31:44.237353Z","snippet":null,"locator":"accession \"PDC000114\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"35931981","pmcid":"PMC9354326","doi":"10.1186/s12859-022-04864-y","title":"DAGBagM: learning directed acyclic graphs of mixed variables with an application to identify protein biomarkers for treatment response in ovarian cancer.","journal":"BMC bioinformatics","year":2022,"authors_short":"Chowdhury et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/35931981/","is_open_access":true,"citation_count":9,"evidence":[]},"tier":"t2_declared","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","author_keys":["birrer m","chowdhury s","gygi s","huntoon c","karnitz l","kaufmann s","paulovich a","peng j","wang p","wang r"],"nci_funded_reuse":true,"linked_grants":["U24CA271114","U24CA210993","U01CA214114","P50CA136393"],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DATA_AVAILABILITY:\"PDC000114\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:31:44.237353Z","snippet":null,"locator":"accession \"PDC000114\" indexed in DATA_AVAILABILITY","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]}],"reuse_metrics":{"n_candidates_screened":7,"n_by_tier":{"t3_analyzed":7,"t2_declared":2,"t1_accession":0,"t0_mention":0},"n_by_tier_raw":{"t3_analyzed":7,"t2_declared":2,"t1_accession":0,"t0_mention":0},"accession_precision":{"token":"PDC000114","query":"METHODS:\"PDC000114\"","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":7,"n_reuse_examined":9,"n_independent_reuse":0,"n_nci_funded_reuse":1,"first_reuse_year":2022,"latest_reuse_year":2025,"years_since_release":4.72,"expected_reuse":3.71,"reuse_gap_index":0.764,"reuse_gap_percentile":66.7,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:49.042869Z","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":"2026-09-20T18:07:49.042869Z","snippet":null,"locator":"tokens: PDC000114; queries: METHODS:\"PDC000114\"; DATA_AVAILABILITY:\"PDC000114\"; ACCESSION_ID:\"PDC000114\"; REF:\"PDC000114\"","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":"2026-09-20T18:16:12.387812Z","snippet":null,"locator":"first referenced in 2022 (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 +0.76)."],"index_value":0.764,"percentile":66.7,"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":"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":4522764,"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":"2026-09-18T03:31:44.347700Z","snippet":null,"locator":"PMID 35931981 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 study."}]},{"core_project_num":"U24CA210993","project_num":null,"title":"Systems Biology based Proteogenomic Translator for Cancer Marker Discovery towards Precision Medicine","pi_names":["ERIC E SCHADT","Pei Wang"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":4643922,"org_name":"ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210993","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T03:31:44.347700Z","snippet":null,"locator":"PMID 35931981 reported under U24CA210993","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":"U01CA214114","project_num":null,"title":"Proteogenomic studies aimed at understanding ovarian tumor responses to agents targeting the DNA damage response and translating this knowledge into clinical benefit","pi_names":["Michael Birrer","AMANDA G PAULOVICH"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2017,2018,2019,2020,2021],"award_amount_usd":8409202,"org_name":"FRED HUTCHINSON CANCER CENTER","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA214114","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T03:31:44.347700Z","snippet":null,"locator":"PMID 35931981 reported under U01CA214114","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":"P50CA136393","project_num":null,"title":"Personalized Vaccines Targeting Cryptic Antigens in Ovarian Cancer","pi_names":["Marion Curtis","Jamie N Bakkum-Gamez","SCOTT H KAUFMANN","Saravut Weroha","Ann Laura Oberg","Keith L. Knutson","ELLEN L. GOODE","Yajue Huang","Zhenkun Lou","Alexandre Gaspar Maia","WILLIAM A CLIBY","LARRY M KARNITZ","Branden S Moriarity","Matthew Stephen Block","MARK E SHERMAN","Fergus Joseph Couch","Gary L Keeney","Ernst Lengyel","Alan P. Fields","PAUL HALUSKA","Evanthia Galanis","KAH-WHYE PENG","Harry Long","KEITH C. BIBLE","VIJI SHRIDHAR","Debra Bell","Wilma Lingle","LYNN C. HARTMANN"],"agency_ic":"NCI","activity_code":"P50","fiscal_years":[2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2021,2022,2023,2024,2025,2026],"award_amount_usd":68946015,"org_name":"MAYO CLINIC ROCHESTER","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P50CA136393","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T03:31:44.347700Z","snippet":null,"locator":"PMID 35931981 reported under P50CA136393","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":"Open the study in the PDC portal","detail":"Proteomic data are released open; the portal's use guidelines still apply.","url":"https://pdc.cancer.gov/pdc/study/PDC000114","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/study/PDC000114","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.435585Z","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":2,"action":"Accept the data use guidelines and download","detail":"The portal asks for acknowledgement and citation, not a data access request.","url":"https://pdc.cancer.gov/pdc/data-use-guidelines","requires":[],"est_time":"minutes to hours, by study size","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/data-use-guidelines","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.435588Z","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":"Resolve the study UUID, then fetch the file manifest","detail":"filesPerStudy keys on the study UUID, not on PDC000114: 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=\"PDC000114\")[\"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":"2026-09-21T12:30:59.435590Z","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-tcga-ovarian-pnnl-proteome.json","jsonld_url":"/data/jsonld/pdc-tcga-ovarian-pnnl-proteome.jsonld","croissant_url":"/data/croissant/pdc-tcga-ovarian-pnnl-proteome.json","instructions_url":"/data/agent/pdc-tcga-ovarian-pnnl-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}