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Flagged for expert review before being relied on."}]}],"reuse":[{"publication":{"pmid":"41107806","pmcid":"PMC12535109","doi":"10.1186/s12905-025-04039-w","title":"Lactate dehydrogenase a is a crucial biomarker that affects the prognosis, chemotherapy effect, and immune infiltration of breast cancer.","journal":"BMC women's health","year":2025,"authors_short":"Xia et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/41107806/","is_open_access":true,"citation_count":4,"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":"RESULTS","author_keys":["dou h","gao t","jia s","luo d","wang j","wang y","xia j","xiao m"],"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=RESULTS:\"PDC000248\"","source_label":"Europe PMC section search (RESULTS)","retrieved_at":"2026-09-18T03:24:13.638438Z","snippet":null,"locator":"accession \"PDC000248\" indexed in RESULTS","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":"41881953","pmcid":"PMC13039154","doi":"10.1038/s41419-026-08642-z","title":"CAFs-derived LAM332 promotes CTCs formation and survival via ITGA3 and contributes to the metastasis of pancreatic ductal adenocarcinoma.","journal":"Cell death & disease","year":2026,"authors_short":"Tang et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/41881953/","is_open_access":true,"citation_count":2,"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":["gao s","lei z","shi w","tan s","tang h","wang y","zhang q","zhang z","zhou j","zhou p"],"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:\"PDC000248\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:24:13.638438Z","snippet":null,"locator":"accession \"PDC000248\" 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":"41402909","pmcid":"PMC12821902","doi":"10.1186/s13058-025-02195-3","title":"MAP3K1/MAP2K4 mutations drive breast cancer progression by compensating for TP53 loss through inactivation of the JNK2-p53-FOSL1 axis.","journal":"Breast cancer research : BCR","year":2025,"authors_short":"Hu et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/41402909/","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":"DATA_AVAILABILITY, METHODS","author_keys":["gao r","sun l","wang m","zhang 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:\"PDC000248\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:24:13.638438Z","snippet":null,"locator":"accession \"PDC000248\" 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":3,"n_by_tier":{"t3_analyzed":3,"t2_declared":1,"t1_accession":0,"t0_mention":0},"n_by_tier_raw":{"t3_analyzed":3,"t2_declared":1,"t1_accession":0,"t0_mention":0},"accession_precision":{"token":"PDC000248","query":"METHODS:\"PDC000248\"","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":4,"n_independent_reuse":0,"n_nci_funded_reuse":0,"first_reuse_year":2025,"latest_reuse_year":2026,"years_since_release":1.72,"expected_reuse":0.32,"reuse_gap_index":1.6,"reuse_gap_percentile":85.6,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:48.577209Z","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":"2026-09-20T18:07:48.577209Z","snippet":null,"locator":"tokens: PDC000248; queries: METHODS:\"PDC000248\"; DATA_AVAILABILITY:\"PDC000248\"; ACCESSION_ID:\"PDC000248\"; REF:\"PDC000248\"","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":"2026-09-20T18:13:04.269019Z","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 +1.60)."],"index_value":1.6,"percentile":85.6,"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":[],"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/PDC000248","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/study/PDC000248","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.432621Z","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":"2026-09-21T12:30:59.432623Z","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 PDC000248: 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=\"PDC000248\")[\"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":"2026-09-21T12:30:59.432625Z","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-ku-pdac-discovery-study-global-proteome.json","jsonld_url":"/data/jsonld/pdc-ku-pdac-discovery-study-global-proteome.jsonld","croissant_url":"/data/croissant/pdc-ku-pdac-discovery-study-global-proteome.json","instructions_url":"/data/agent/pdc-ku-pdac-discovery-study-global-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":32.1,"tags":["pdc","proteogenomics"],"search_text":null}