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Medicine","year":2024,"authors_short":"Pino et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/38232702/","is_open_access":true,"citation_count":21,"evidence":[{"method":"derived","source_url":null,"source_label":"Candidate primary publication (machine-inferred)","retrieved_at":"2026-09-20T18:12:46.173736Z","snippet":null,"locator":"earliest highly cited article analyzing PDC000478 (published 2024)","confidence":"low","reviewer":null,"reviewed_at":null,"note":"Inferred, not authoritative. The source repository does not publish a marker-paper link for this dataset, so we nominate the earliest heavily cited article that analyzed it. Flagged for expert review before being relied on."}]}],"reuse":[{"publication":{"pmid":"38584833","pmcid":"PMC10997032","doi":"10.1515/med-2024-0944","title":"High SEC61A1 expression predicts poor outcome of acute myeloid leukemia.","journal":"Open medicine (Warsaw, Poland)","year":2024,"authors_short":"Ji et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/38584833/","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":["yang x"],"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:\"PDC000478\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:20:55.327265Z","snippet":null,"locator":"accession \"PDC000478\" 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."}]}],"reuse_metrics":{"n_candidates_screened":2,"n_by_tier":{"t3_analyzed":2,"t2_declared":0,"t1_accession":0,"t0_mention":0},"n_by_tier_raw":{"t3_analyzed":2,"t2_declared":0,"t1_accession":0,"t0_mention":0},"accession_precision":{"token":"PDC000477","query":"METHODS:\"PDC000477\"","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":2,"n_reuse_examined":2,"n_independent_reuse":0,"n_nci_funded_reuse":0,"first_reuse_year":2024,"latest_reuse_year":2024,"years_since_release":2.72,"expected_reuse":4.74,"reuse_gap_index":-0.935,"reuse_gap_percentile":27.3,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:48.299206Z","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":"2026-09-20T18:07:48.299206Z","snippet":null,"locator":"tokens: PDC000478, PDC000477; queries: METHODS:\"PDC000477\"; DATA_AVAILABILITY:\"PDC000478\"; ACCESSION_ID:\"PDC000478\"; REF:\"PDC000478\"","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":"2026-09-20T18:12:46.173736Z","snippet":null,"locator":"first referenced in 2024 (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 -0.94)."],"index_value":-0.935,"percentile":27.3,"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. This record spans 2 PDC studies; repeat for each.","url":"https://pdc.cancer.gov/pdc/study/PDC000478","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/study/PDC000478","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.431713Z","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":"2026-09-21T12:30:59.431715Z","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 PDC000478: 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=\"PDC000478\")[\"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":"2026-09-21T12:30:59.431717Z","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-beat-aml-baseline-clinical.json","jsonld_url":"/data/jsonld/pdc-beat-aml-baseline-clinical.jsonld","croissant_url":"/data/croissant/pdc-beat-aml-baseline-clinical.json","instructions_url":"/data/agent/pdc-beat-aml-baseline-clinical.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}