{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37874388", "kind": "science-record", "revision": 4, "content_hash": "sha256:2855802460b2e6385d0d5ba114e4fd9180c11eed9e666446331eccca19c5d99a", "created_at": "2026-11-01T19:02:44Z", "updated_at": "2026-11-01T22:52:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A risk score model based on lipid metabolism-related genes could predict response to immunotherapy and prognosis of lung adenocarcinoma: a multi-dataset study and cytological validation.", "doi": "10.1007/s12672-023-00802-3", "pmid": "37874388", "authors": ["Yangyang Lei", "Boxuan Zhou", "Xiangzhi Meng", "Mei Liang", "Weijian Song", "Yicheng Liang", "Yushun Gao", "Minghui Wang"], "journal": "Discover oncology", "year": 2023, "abstract": "BACKGROUND: Lipid metabolism is a key factor in tumorigenesis and drug resistance, and models related to lipid metabolism have shown potential to predict survival and curative effects of adjuvant therapy in various cancers. However, the relationship between lipid metabolism and prognosis and treatment response of lung adenocarcinoma (LUAD) are still unclear.\nMETHODS: We enrolled seven bulk RNA-sequence datasets (GSE37745, GSE19188, GSE30219, GSE31547, GSE41271, GSE42127, and GSE72094) from the GEO database and one single-cell RNA-sequencing dataset (GSE117570) from the TISCH2 database. Non-negative matrix factorization (NMF) was utilized to construct the risk score model based on lipid score calculated by GSVA algorithm. Phs000452.v3, PMID: 26359337, PMID: 32472114, PRJEB23709 datasets were used to test the response to immunotherapy. Drug sensitivity analysis was assessed according to the GDSC database, and immunotherapy response was evaluated using the Wilcoxon test. Cellular function assays including clone formation, EDU assays and flow cytometry were implemented to explore the phenotype alteration caused by the knockdown of PTDSS1, which is one of key gene in risk score model.\nRESULTS: We analyzed both bulk and single-cell RNA sequencing data to establish and validate a risk score model based on 18 lipid metabolism-related genes with significant impact on prognosis. After divided the patients into two groups according to risk score, we identified differences in lipid-related metabolic processes and a detailed portrait of the immune landscapes of high- and low-risk groups. Moreover, we investigated the potentials of our risk score in predicting response to immunotherapy and drug sensitivity. In addition, we silenced PTDSS1 in LUAD cell lines, and found that the proliferation of the cells was weakened, and the apoptosis of the cells was increased.\nCONCLUSION: Our study highlights the crucial roles of lipid metabolism in LUAD and provides a reliable risk score model, which can aid in predicting prognosis and response to immunotherapy. Furthermore, we investigated the roles of PTDSS1 in LUAD carcinogenesis, which showed that PTDSS1 regulated proliferation and apoptosis of LUAD cells.", "claims": [{"id": "claim-method", "statement": "We performed univariate cox regression on all lipid metabolism-related genes to evaluate their impacts on the prognosis of LUAD patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37874388", "locator": "sections[17] \"Prognostic analysis and model construction of lipid-score\" paragraph 2", "quote": "We performed univariate cox regression on all lipid metabolism-related genes to evaluate their impacts on the prognosis of LUAD patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data can be obtained from the corresponding author when required.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37874388", "locator": "sections[29] \"Data availability\" paragraph 2", "quote": "Data can be obtained from the corresponding author when required."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our study highlights the crucial roles of lipid metabolism in LUAD and provides a reliable risk score model, which can aid in predicting prognosis and response to immunotherapy.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37874388", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our study highlights the crucial roles of lipid metabolism in LUAD and provides a reliable risk score model, which can aid in predicting prognosis and response to immunotherapy."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our study highlights the crucial roles of lipid metabolism in LUAD and provides a reliable risk score model, which can aid in predicting prognosis and response to immunotherapy.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:37874388"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE117570"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE117570"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37874388", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-023-00802-3", "sha256": "sha256:0569a32cc257243058302a5c70835a28c7d7db34fac94ddca8cce04de6f4b80a", "bytes": 36561, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-023-00802-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10597940", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE117570", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117570", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE117570", "version": null, "note": "Data can be obtained from the corresponding author when required.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data can be obtained from the corresponding author when required.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3304007", "GSM3304008", "GSM3304009", "GSM3304010", "GSM3304011", "GSM3304012", "GSM3304013", "GSM3304014"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Reprogramming of Tumor-infiltrating Immune Cells in Early Stage of NSCLC", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE19188", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19188", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19188", "version": null, "note": "Data can be obtained from the corresponding author when required.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data can be obtained from the corresponding author when required.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM475656", "GSM475657", "GSM475658", "GSM475659", "GSM475660", "GSM475661", "GSM475662", "GSM475663", "GSM475664", "GSM475665", "GSM475666", "GSM475667", "GSM475668", "GSM475669", "GSM475670", "GSM475671", "GSM475672", "GSM475673", "GSM475674", "GSM475675", "GSM475676", "GSM475677", "GSM475678", "GSM475679", "GSM475680", "GSM475681", "GSM475682", "GSM475683", "GSM475684", "GSM475685", "GSM475686", "GSM475687", "GSM475688", "GSM475689", "GSM475690", "GSM475691", "GSM475692", "GSM475693", "GSM475694", "GSM475695", "GSM475696", "GSM475697", "GSM475698", "GSM475699", "GSM475700", "GSM475701", "GSM475702", "GSM475703", "GSM475704", "GSM475705", "GSM475706", "GSM475707", "GSM475708", "GSM475709", "GSM475710", "GSM475711", "GSM475712", "GSM475713", "GSM475714", "GSM475715", "GSM475716", "GSM475717", "GSM475718", "GSM475719", "GSM475720", "GSM475721", "GSM475722", "GSM475723", "GSM475724", "GSM475725", "GSM475726", "GSM475727", "GSM475728", "GSM475729", "GSM475730", "GSM475731", "GSM475732", "GSM475733", "GSM475734", "GSM475735", "GSM475736", "GSM475737", "GSM475738", "GSM475739", "GSM475740", "GSM475741", "GSM475742", "GSM475743", "GSM475744", "GSM475745", "GSM475746", "GSM475747", "GSM475748", "GSM475749", "GSM475750", "GSM475751", "GSM475752", "GSM475753", "GSM475754", "GSM475755", "GSM475756", "GSM475757", "GSM475758", "GSM475759", "GSM475760", "GSM475761", "GSM475762", "GSM475763", "GSM475764", "GSM475765", "GSM475766", "GSM475767", "GSM475768", "GSM475769", "GSM475770", "GSM475771", "GSM475772", "GSM475773", "GSM475774", "GSM475775", "GSM475776", "GSM475777", "GSM475778", "GSM475779", "GSM475780", "GSM475781", "GSM475782", "GSM475783", "GSM475784", "GSM475785", "GSM475786", "GSM475787", "GSM475788", "GSM475789", "GSM475790", "GSM475791", "GSM475792", "GSM475793", "GSM475794", "GSM475795", "GSM475796", "GSM475797", "GSM475798", "GSM475799", "GSM475800", "GSM475801", "GSM475802", "GSM475803", "GSM475804", "GSM475805", "GSM475806", "GSM475807", "GSM475808", "GSM475809", "GSM475810", "GSM475811"], "sample_count": 156, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data for early stage NSCLC", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE30219", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30219", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30219", "version": null, "note": "Data can be obtained from the corresponding author when required.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data can be obtained from the corresponding author when required.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1465989", "GSM1465990", "GSM1465991", "GSM1465992", "GSM1465993", "GSM1465994", "GSM1465995", "GSM1465996", "GSM1465997", "GSM1465998", "GSM1465999", "GSM748053", "GSM748054", "GSM748055", "GSM748056", "GSM748057", "GSM748058", "GSM748059", "GSM748060", "GSM748061", "GSM748062", "GSM748063", "GSM748064", "GSM748065", "GSM748066", "GSM748067", "GSM748068", "GSM748069", "GSM748070", "GSM748071", "GSM748072", "GSM748073", "GSM748074", "GSM748075", "GSM748076", "GSM748077", "GSM748078", "GSM748079", "GSM748080", "GSM748081", "GSM748083", "GSM748084", "GSM748085", "GSM748086", "GSM748087", "GSM748088", "GSM748089", "GSM748090", "GSM748091", "GSM748092", "GSM748093", "GSM748094", "GSM748095", "GSM748096", "GSM748097", "GSM748098", "GSM748099", "GSM748100", "GSM748101", "GSM748102", "GSM748103", "GSM748104", "GSM748105", "GSM748106", "GSM748107", "GSM748108", "GSM748109", "GSM748110", "GSM748111", "GSM748112", "GSM748113", "GSM748115", "GSM748116", "GSM748117", "GSM748118", "GSM748119", "GSM748120", "GSM748121", "GSM748122", "GSM748123", "GSM748124", "GSM748125", "GSM748126", "GSM748127", "GSM748128", "GSM748129", "GSM748130", "GSM748131", "GSM748132", "GSM748133", "GSM748134", "GSM748135", "GSM748136", "GSM748137", "GSM748138", "GSM748139", "GSM748140", "GSM748141", "GSM748142", "GSM748143", "GSM748144", "GSM748145", "GSM748146", "GSM748147", "GSM748148", "GSM748149", "GSM748150", "GSM748151", "GSM748152", "GSM748153", "GSM748154", "GSM748155", "GSM748156", "GSM748157", "GSM748158", "GSM748159", "GSM748160", "GSM748161", "GSM748162", "GSM748163", "GSM748164", "GSM748165", "GSM748166", "GSM748167", "GSM748168", "GSM748169", "GSM748170", "GSM748171", "GSM748172", "GSM748173", "GSM748174", "GSM748175", "GSM748176", "GSM748177", "GSM748178", "GSM748179", "GSM748180", "GSM748181", "GSM748182", "GSM748183", "GSM748184", "GSM748185", "GSM748186", "GSM748187", "GSM748188", "GSM748189", "GSM748191", "GSM748192", "GSM748193", "GSM748195", "GSM748196", "GSM748197", "GSM748198", "GSM748199", "GSM748200", "GSM748201", "GSM748202", "GSM748203", "GSM748206", "GSM748207", "GSM748209", "GSM748210", "GSM748211", "GSM748212", "GSM748213", "GSM748214", "GSM748215", "GSM748216", "GSM748217", "GSM748218", "GSM748219", "GSM748220", "GSM748221", "GSM748222", "GSM748223", "GSM748224", "GSM748225", "GSM748226", "GSM748227", "GSM748228", "GSM748229", "GSM748232", "GSM748233", "GSM748234", "GSM748235", "GSM748239", "GSM748240", "GSM748242", "GSM748243", "GSM748244", "GSM748245", "GSM748246", "GSM748247", "GSM748248", "GSM748249", "GSM748250", "GSM748251", "GSM748252", "GSM748253", "GSM748254", "GSM748255", "GSM748256", "GSM748257", "GSM748258", "GSM748259", "GSM748260", "GSM748261", "GSM748262", "GSM748263", "GSM748264", "GSM748265", "GSM748266", "GSM748267", "GSM748268", "GSM748269", "GSM748270", "GSM748271", "GSM748272", "GSM748273", "GSM748274", "GSM748275", "GSM748276", "GSM748277", "GSM748278", "GSM748279", "GSM748280", "GSM748281", "GSM748282", "GSM748283", "GSM748284", "GSM748285", "GSM748286", "GSM748287", "GSM748288", "GSM748291", "GSM748292", "GSM748294", "GSM748295", "GSM748296", "GSM748297", "GSM748298", "GSM748299", "GSM748300", "GSM748301", "GSM748302", "GSM748303", "GSM748304", "GSM748305", "GSM748306", "GSM748307", "GSM748308", "GSM748309", "GSM748310", "GSM748311", "GSM748312", "GSM748313", "GSM748314", "GSM748315", "GSM748316", "GSM748317", "GSM748318", "GSM748319", "GSM748320", "GSM748321", "GSM748323", "GSM748324", "GSM748325", "GSM748326", "GSM748327", "GSM748328", "GSM748329", "GSM748330", "GSM748331", "GSM748332", "GSM748333", "GSM748334", "GSM748335", "GSM748336", "GSM748337", "GSM748338", "GSM748339", "GSM748341", "GSM748342", "GSM748343", "GSM748344", "GSM748345", "GSM748346", "GSM748347", "GSM748348", "GSM748349", "GSM748350", "GSM748351", "GSM748352", "GSM748353", "GSM748354", "GSM748355", "GSM748356", "GSM748357", "GSM748358", "GSM748359", "GSM748360", "GSM748361", "GSM748362", "GSM748363", "GSM748364", "GSM748365", "GSM748366"], "sample_count": 307, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "\"Off-context\" gene expression in lung cancer identifies a group of metastatic-prone tumors", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE31547", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31547", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31547", "version": null, "note": "Data can be obtained from the corresponding author when required.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data can be obtained from the corresponding author when required.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM782978", "GSM782979", "GSM782980", "GSM782981", "GSM782982", "GSM782983", "GSM782984", "GSM782985", "GSM782986", "GSM782987", "GSM782988", "GSM782989", "GSM782990", "GSM782991", "GSM782992", "GSM782993", "GSM782994", "GSM782995", "GSM782996", "GSM782997", "GSM782998", "GSM782999", "GSM783000", "GSM783001", "GSM783002", "GSM783003", "GSM783004", "GSM783005", "GSM783006", "GSM783007", "GSM783008", "GSM783009", "GSM783010", "GSM783011", "GSM783012", "GSM783013", "GSM783014", "GSM783015", "GSM783016", "GSM783017", "GSM783018", "GSM783019", "GSM783020", "GSM783021", "GSM783022", "GSM783023", "GSM783024", "GSM783025", "GSM783026", "GSM783027"], "sample_count": 50, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "MSKCC-A Primary Lung Cancer Specimens", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE37745", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37745", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37745", "version": null, "note": "Data can be obtained from the corresponding author when required.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data can be obtained from the corresponding author when required.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1019138", "GSM1019139", "GSM1019140", "GSM1019141", "GSM1019142", "GSM1019143", "GSM1019144", "GSM1019145", "GSM1019146", "GSM1019147", "GSM1019148", "GSM1019149", "GSM1019150", "GSM1019151", "GSM1019152", "GSM1019153", "GSM1019154", "GSM1019155", "GSM1019156", "GSM1019157", "GSM1019158", "GSM1019159", "GSM1019160", "GSM1019161", "GSM1019162", "GSM1019163", "GSM1019164", "GSM1019165", "GSM1019166", "GSM1019167", "GSM1019168", "GSM1019169", "GSM1019170", "GSM1019171", "GSM1019172", "GSM1019173", "GSM1019174", "GSM1019175", "GSM1019176", "GSM1019177", "GSM1019178", "GSM1019179", "GSM1019180", "GSM1019181", "GSM1019182", "GSM1019183", "GSM1019184", "GSM1019185", "GSM1019186", "GSM1019187", "GSM1019188", "GSM1019189", "GSM1019190", "GSM1019191", "GSM1019192", "GSM1019193", "GSM1019194", "GSM1019195", "GSM1019196", "GSM1019197", "GSM1019198", "GSM1019199", "GSM1019200", "GSM1019201", "GSM1019202", "GSM1019203", "GSM1019204", "GSM1019205", "GSM1019206", "GSM1019207", "GSM1019208", "GSM1019209", "GSM1019210", "GSM1019211", "GSM1019212", "GSM1019213", "GSM1019214", "GSM1019215", "GSM1019216", "GSM1019217", "GSM1019218", "GSM1019219", "GSM1019220", "GSM1019221", "GSM1019222", "GSM1019223", "GSM1019224", "GSM1019225", "GSM1019226", "GSM1019227", "GSM1019228", "GSM1019229", "GSM1019230", "GSM1019231", "GSM1019232", "GSM1019233", "GSM1019234", "GSM1019235", "GSM1019236", "GSM1019237", "GSM1019238", "GSM1019239", "GSM1019240", "GSM1019241", "GSM1019242", "GSM1019243", "GSM1019244", "GSM1019245", "GSM1019246", "GSM1019247", "GSM1019248", "GSM1019249", "GSM1019250", "GSM1019251", "GSM1019252", "GSM1019253", "GSM1019254", "GSM1019255", "GSM1019256", "GSM1019257", "GSM1019258", "GSM1019259", "GSM1019260", "GSM1019261", "GSM1019262", "GSM1019263", "GSM1019264", "GSM1019265", "GSM1019266", "GSM1019267", "GSM1019268", "GSM1019269", "GSM1019270", "GSM1019271", "GSM1019272", "GSM1019273", "GSM1019274", "GSM1019275", "GSM1019276", "GSM1019277", "GSM1019278", "GSM1019279", "GSM1019280", "GSM1019281", "GSM1019282", "GSM1019283", "GSM1019284", "GSM1019285", "GSM1019286", "GSM1019287", "GSM1019288", "GSM1019289", "GSM1019290", "GSM1019291", "GSM1019292", "GSM1019293", "GSM1019294", "GSM1019295", "GSM1019296", "GSM1019297", "GSM1019298", "GSM1019299", "GSM1019300", "GSM1019301", "GSM1019302", "GSM1019303", "GSM1019304", "GSM1019305", "GSM1019306", "GSM1019307", "GSM1019308", "GSM1019309", "GSM1019310", "GSM1019311", "GSM1019312", "GSM1019313", "GSM1019314", "GSM1019315", "GSM1019316", "GSM1019317", "GSM1019318", "GSM1019319", "GSM1019320", "GSM1019321", "GSM1019322", "GSM1019323", "GSM1019324", "GSM1019325", "GSM1019326", "GSM1019327", "GSM1019328", "GSM1019329", "GSM1019330", "GSM1019331", "GSM1019332", "GSM1019333"], "sample_count": 196, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis and tissue microarray validation", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE41271", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41271", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41271", "version": null, "note": "Data can be obtained from the corresponding author when required.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data can be obtained from the corresponding author when required.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1012828", "GSM1012829", "GSM1012830", "GSM1012831", "GSM1012832", "GSM1012833", "GSM1012834", "GSM1012835", "GSM1012836", "GSM1012837", "GSM1012838", "GSM1012839", "GSM1012840", "GSM1012841", "GSM1012842", "GSM1012843", "GSM1012844", "GSM1012845", "GSM1012846", "GSM1012847", "GSM1012848", "GSM1012849", "GSM1012850", "GSM1012851", "GSM1012852", "GSM1012853", "GSM1012854", "GSM1012855", "GSM1012856", "GSM1012857", "GSM1012858", "GSM1012859", "GSM1012860", "GSM1012861", "GSM1012862", "GSM1012863", "GSM1012864", "GSM1012865", "GSM1012866", "GSM1012867", "GSM1012868", "GSM1012869", "GSM1012870", "GSM1012871", "GSM1012872", "GSM1012873", "GSM1012874", "GSM1012875", "GSM1012876", "GSM1012877", "GSM1012878", "GSM1012879", "GSM1012880", "GSM1012881", "GSM1012882", "GSM1012883", "GSM1012884", "GSM1012885", "GSM1012886", "GSM1012887", "GSM1012888", "GSM1012889", "GSM1012890", "GSM1012891", "GSM1012892", "GSM1012893", "GSM1012894", "GSM1012895", "GSM1012896", "GSM1012897", "GSM1012898", "GSM1012899", "GSM1012900", "GSM1012901", "GSM1012902", "GSM1012903", "GSM1012904", "GSM1012905", "GSM1012906", "GSM1012907", "GSM1012908", "GSM1012909", "GSM1012910", "GSM1012911", "GSM1012912", "GSM1012913", "GSM1012914", "GSM1012915", "GSM1012916", "GSM1012917", "GSM1012918", "GSM1012919", "GSM1012920", "GSM1012921", "GSM1012922", "GSM1012923", "GSM1012924", "GSM1012925", "GSM1012926", "GSM1012927", "GSM1012928", "GSM1012929", "GSM1012930", "GSM1012931", "GSM1012932", "GSM1012933", "GSM1012934", "GSM1012935", "GSM1012936", "GSM1012937", "GSM1012938", "GSM1012939", "GSM1012940", "GSM1012941", "GSM1012942", "GSM1012943", "GSM1012944", "GSM1012945", "GSM1012946", "GSM1012947", "GSM1012948", "GSM1012949", "GSM1012950", "GSM1012951", "GSM1012952", "GSM1012953", "GSM1012954", "GSM1012955", "GSM1012956", "GSM1012957", "GSM1012958", "GSM1012959", "GSM1012960", "GSM1012961", "GSM1012962", "GSM1012963", "GSM1012964", "GSM1012965", "GSM1012966", "GSM1012967", "GSM1012968", "GSM1012969", "GSM1012970", "GSM1012971", "GSM1012972", "GSM1012973", "GSM1012974", "GSM1012975", "GSM1012976", "GSM1012977", "GSM1012978", "GSM1012979", "GSM1012980", "GSM1012981", "GSM1012982", "GSM1012983", "GSM1012984", "GSM1012985", "GSM1012986", "GSM1012987", "GSM1012988", "GSM1012989", "GSM1012990", "GSM1012991", "GSM1012992", "GSM1012993", "GSM1012994", "GSM1012995", "GSM1012996", "GSM1012997", "GSM1012998", "GSM1012999", "GSM1013000", "GSM1013001", "GSM1013002", "GSM1013003", "GSM1013004", "GSM1013005", "GSM1013006", "GSM1013007", "GSM1013008", "GSM1013009", "GSM1013010", "GSM1013011", "GSM1013012", "GSM1013013", "GSM1013014", "GSM1013015", "GSM1013016", "GSM1013017", "GSM1013018", "GSM1013019", "GSM1013020", "GSM1013021", "GSM1013022", "GSM1013023", "GSM1013024", "GSM1013025", "GSM1013026", "GSM1013027", "GSM1013028", "GSM1013029", "GSM1013030", "GSM1013031", "GSM1013032", "GSM1013033", "GSM1013034", "GSM1013035", "GSM1013036", "GSM1013037", "GSM1013038", "GSM1013039", "GSM1013040", "GSM1013041", "GSM1013042", "GSM1013043", "GSM1013044", "GSM1013045", "GSM1013046", "GSM1013047", "GSM1013048", "GSM1013049", "GSM1013050", "GSM1013051", "GSM1013052", "GSM1013053", "GSM1013054", "GSM1013055", "GSM1013056", "GSM1013057", "GSM1013058", "GSM1013059", "GSM1013060", "GSM1013061", "GSM1013062", "GSM1013063", "GSM1013064", "GSM1013065", "GSM1013066", "GSM1013067", "GSM1013068", "GSM1013069", "GSM1013070", "GSM1013071", "GSM1013072", "GSM1013073", "GSM1013074", "GSM1013075", "GSM1013076", "GSM1013077", "GSM1013078", "GSM1013079", "GSM1013080", "GSM1013081", "GSM1013082", "GSM1013083", "GSM1013084", "GSM1013085", "GSM1013086", "GSM1013087", "GSM1013088", "GSM1013089", "GSM1013090", "GSM1013091", "GSM1013092", "GSM1013093", "GSM1013094", "GSM1013095", "GSM1013096", "GSM1013097", "GSM1013098", "GSM1013099", "GSM1013100", "GSM1013101", "GSM1013102"], "sample_count": 275, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Expression profiling of 275 lung cancer specimens", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE42127", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42127", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE42127", "version": null, "note": "Data can be obtained from the corresponding author when required.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data can be obtained from the corresponding author when required.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1032881", "GSM1032882", "GSM1032883", "GSM1032884", "GSM1032885", "GSM1032886", "GSM1032887", "GSM1032888", "GSM1032889", "GSM1032890", "GSM1032891", "GSM1032892", "GSM1032893", "GSM1032894", "GSM1032895", "GSM1032896", "GSM1032897", "GSM1032898", "GSM1032899", "GSM1032900", "GSM1032901", "GSM1032902", "GSM1032903", "GSM1032904", "GSM1032905", "GSM1032906", "GSM1032907", "GSM1032908", "GSM1032909", "GSM1032910", "GSM1032911", "GSM1032912", "GSM1032913", "GSM1032914", "GSM1032915", "GSM1032916", "GSM1032917", "GSM1032918", "GSM1032919", "GSM1032920", "GSM1032921", "GSM1032922", "GSM1032923", "GSM1032924", "GSM1032925", "GSM1032926", "GSM1032927", "GSM1032928", "GSM1032929", "GSM1032930", "GSM1032931", "GSM1032932", "GSM1032933", "GSM1032934", "GSM1032935", "GSM1032936", "GSM1032937", "GSM1032938", "GSM1032939", "GSM1032940", "GSM1032941", "GSM1032942", "GSM1032943", "GSM1032944", "GSM1032945", "GSM1032946", "GSM1032947", "GSM1032948", "GSM1032949", "GSM1032950", "GSM1032951", "GSM1032952", "GSM1032953", "GSM1032954", "GSM1032955", "GSM1032956", "GSM1032957", "GSM1032958", "GSM1032959", "GSM1032960", "GSM1032961", "GSM1032962", "GSM1032963", "GSM1032964", "GSM1032965", "GSM1032966", "GSM1032967", "GSM1032968", "GSM1032969", "GSM1032970", "GSM1032971", "GSM1032972", "GSM1032973", "GSM1032974", "GSM1032975", "GSM1032976", "GSM1032977", "GSM1032978", "GSM1032979", "GSM1032980", "GSM1032981", "GSM1032982", "GSM1032983", "GSM1032984", "GSM1032985", "GSM1032986", "GSM1032987", "GSM1032988", "GSM1032989", "GSM1032990", "GSM1032991", "GSM1032992", "GSM1032993", "GSM1032994", "GSM1032995", "GSM1032996", "GSM1032997", "GSM1032998", "GSM1032999", "GSM1033000", "GSM1033001", "GSM1033002", "GSM1033003", "GSM1033004", "GSM1033005", "GSM1033006", "GSM1033007", "GSM1033008", "GSM1033009", "GSM1033010", "GSM1033011", "GSM1033012", "GSM1033013", "GSM1033014", "GSM1033015", "GSM1033016", "GSM1033017", "GSM1033018", "GSM1033019", "GSM1033020", "GSM1033021", "GSM1033022", "GSM1033023", "GSM1033024", "GSM1033025", "GSM1033026", "GSM1033027", "GSM1033028", "GSM1033029", "GSM1033030", "GSM1033031", "GSM1033032", "GSM1033033", "GSM1033034", "GSM1033035", "GSM1033036", "GSM1033037", "GSM1033038", "GSM1033039", "GSM1033040", "GSM1033041", "GSM1033042", "GSM1033043", "GSM1033044", "GSM1033045", "GSM1033046", "GSM1033047", "GSM1033048", "GSM1033049", "GSM1033050", "GSM1033051", "GSM1033052", "GSM1033053", "GSM1033054", "GSM1033055", "GSM1033056"], "sample_count": 176, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Expression data for non-small-cell lung cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE72094", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72094", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE72094", "version": null, "note": "Data can be obtained from the corresponding author when required.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data can be obtained from the corresponding author when required.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1854797", "GSM1854798", "GSM1854799", "GSM1854800", "GSM1854801", "GSM1854802", "GSM1854803", "GSM1854804", "GSM1854805", "GSM1854806", "GSM1854807", "GSM1854808", "GSM1854809", "GSM1854810", "GSM1854811", "GSM1854812", "GSM1854813", "GSM1854814", "GSM1854815", "GSM1854816", "GSM1854817", "GSM1854818", "GSM1854819", "GSM1854820", "GSM1854821", "GSM1854822", "GSM1854823", "GSM1854824", "GSM1854825", "GSM1854826", "GSM1854827", "GSM1854828", "GSM1854829", "GSM1854830", "GSM1854831", "GSM1854832", "GSM1854833", "GSM1854834", "GSM1854835", "GSM1854836", "GSM1854837", "GSM1854838", "GSM1854839", "GSM1854840", "GSM1854841", "GSM1854842", "GSM1854843", "GSM1854844", "GSM1854845", "GSM1854846", "GSM1854847", "GSM1854848", "GSM1854849", "GSM1854850", "GSM1854851", "GSM1854852", "GSM1854853", "GSM1854854", "GSM1854855", "GSM1854856", "GSM1854857", "GSM1854858", "GSM1854859", "GSM1854860", "GSM1854861", "GSM1854862", "GSM1854863", "GSM1854864", "GSM1854865", "GSM1854866", "GSM1854867", "GSM1854868", "GSM1854869", "GSM1854870", "GSM1854871", "GSM1854872", "GSM1854873", "GSM1854874", "GSM1854875", "GSM1854876", "GSM1854877", "GSM1854878", "GSM1854879", "GSM1854880", "GSM1854881", "GSM1854882", "GSM1854883", "GSM1854884", "GSM1854885", "GSM1854886", "GSM1854887", "GSM1854888", "GSM1854889", "GSM1854890", "GSM1854891", "GSM1854892", "GSM1854893", "GSM1854894", "GSM1854895", "GSM1854896", "GSM1854897", "GSM1854898", "GSM1854899", "GSM1854900", "GSM1854901", "GSM1854902", "GSM1854903", "GSM1854904", "GSM1854905", "GSM1854906", "GSM1854907", "GSM1854908", "GSM1854909", "GSM1854910", "GSM1854911", "GSM1854912", "GSM1854913", "GSM1854914", "GSM1854915", "GSM1854916", "GSM1854917", "GSM1854918", "GSM1854919", "GSM1854920", "GSM1854921", "GSM1854922", "GSM1854923", "GSM1854924", "GSM1854925", "GSM1854926", "GSM1854927", "GSM1854928", "GSM1854929", "GSM1854930", "GSM1854931", "GSM1854932", "GSM1854933", "GSM1854934", "GSM1854935", "GSM1854936", "GSM1854937", "GSM1854938", "GSM1854939", "GSM1854940", "GSM1854941", "GSM1854942", "GSM1854943", "GSM1854944", "GSM1854945", "GSM1854946", "GSM1854947", "GSM1854948", "GSM1854949", "GSM1854950", "GSM1854951", "GSM1854952", "GSM1854953", "GSM1854954", "GSM1854955", "GSM1854956", "GSM1854957", "GSM1854958", "GSM1854959", "GSM1854960", "GSM1854961", "GSM1854962", "GSM1854963", "GSM1854964", "GSM1854965", "GSM1854966", "GSM1854967", "GSM1854968", "GSM1854969", "GSM1854970", "GSM1854971", "GSM1854972", "GSM1854973", "GSM1854974", "GSM1854975", "GSM1854976", "GSM1854977", "GSM1854978", "GSM1854979", "GSM1854980", "GSM1854981", "GSM1854982", "GSM1854983", "GSM1854984", "GSM1854985", "GSM1854986", "GSM1854987", "GSM1854988", "GSM1854989", "GSM1854990", "GSM1854991", "GSM1854992", "GSM1854993", "GSM1854994", "GSM1854995", "GSM1854996", "GSM1854997", "GSM1854998", "GSM1854999", "GSM1855000", "GSM1855001", "GSM1855002", "GSM1855003", "GSM1855004", "GSM1855005", "GSM1855006", "GSM1855007", "GSM1855008", "GSM1855009", "GSM1855010", "GSM1855011", "GSM1855012", "GSM1855013", "GSM1855014", "GSM1855015", "GSM1855016", "GSM1855017", "GSM1855018", "GSM1855019", "GSM1855020", "GSM1855021", "GSM1855022", "GSM1855023", "GSM1855024", "GSM1855025", "GSM1855026", "GSM1855027", "GSM1855028", "GSM1855029", "GSM1855030", "GSM1855031", "GSM1855032", "GSM1855033", "GSM1855034", "GSM1855035", "GSM1855036", "GSM1855037", "GSM1855038", "GSM1855039", "GSM1855040", "GSM1855041", "GSM1855042", "GSM1855043", "GSM1855044", "GSM1855045", "GSM1855046", "GSM1855047", "GSM1855048", "GSM1855049", "GSM1855050", "GSM1855051", "GSM1855052", "GSM1855053", "GSM1855054", "GSM1855055", "GSM1855056", "GSM1855057", "GSM1855058", "GSM1855059", "GSM1855060", "GSM1855061", "GSM1855062", "GSM1855063", "GSM1855064", "GSM1855065", "GSM1855066", "GSM1855067", "GSM1855068", "GSM1855069", "GSM1855070", "GSM1855071", "GSM1855072", "GSM1855073", "GSM1855074", "GSM1855075", "GSM1855076", "GSM1855077", "GSM1855078", "GSM1855079", "GSM1855080", "GSM1855081", "GSM1855082", "GSM1855083", "GSM1855084", "GSM1855085", "GSM1855086", "GSM1855087", "GSM1855088", "GSM1855089", "GSM1855090", "GSM1855091", "GSM1855092", "GSM1855093", "GSM1855094", "GSM1855095", "GSM1855096", "GSM1855097", "GSM1855098", "GSM1855099", "GSM1855100", "GSM1855101", "GSM1855102", "GSM1855103", "GSM1855104", "GSM1855105", "GSM1855106", "GSM1855107", "GSM1855108", "GSM1855109", "GSM1855110", "GSM1855111", "GSM1855112", "GSM1855113", "GSM1855114", "GSM1855115", "GSM1855116", "GSM1855117", "GSM1855118", "GSM1855119", "GSM1855120", "GSM1855121", "GSM1855122", "GSM1855123", "GSM1855124", "GSM1855125", "GSM1855126", "GSM1855127", "GSM1855128", "GSM1855129", "GSM1855130", "GSM1855131", "GSM1855132", "GSM1855133", "GSM1855134", "GSM1855135", "GSM1855136", "GSM1855137", "GSM1855138", "GSM1855139", "GSM1855140", "GSM1855141", "GSM1855142", "GSM1855143", "GSM1855144", "GSM1855145", "GSM1855146", "GSM1855147", "GSM1855148", "GSM1855149", "GSM1855150", "GSM1855151", "GSM1855152", "GSM1855153", "GSM1855154", "GSM1855155", "GSM1855156", "GSM1855157", "GSM1855158", "GSM1855159", "GSM1855160", "GSM1855161", "GSM1855162", "GSM1855163", "GSM1855164", "GSM1855165", "GSM1855166", "GSM1855167", "GSM1855168", "GSM1855169", "GSM1855170", "GSM1855171", "GSM1855172", "GSM1855173", "GSM1855174", "GSM1855175", "GSM1855176", "GSM1855177", "GSM1855178", "GSM1855179", "GSM1855180", "GSM1855181", "GSM1855182", "GSM1855183", "GSM1855184", "GSM1855185", "GSM1855186", "GSM1855187", "GSM1855188", "GSM1855189", "GSM1855190", "GSM1855191", "GSM1855192", "GSM1855193", "GSM1855194", "GSM1855195", "GSM1855196", "GSM1855197", "GSM1855198", "GSM1855199", "GSM1855200", "GSM1855201", "GSM1855202", "GSM1855203", "GSM1855204", "GSM1855205", "GSM1855206", "GSM1855207", "GSM1855208", "GSM1855209", "GSM1855210", "GSM1855211", "GSM1855212", "GSM1855213", "GSM1855214", "GSM1855215", "GSM1855216", "GSM1855217", "GSM1855218", "GSM1855219", "GSM1855220", "GSM1855221", "GSM1855222", "GSM1855223", "GSM1855224", "GSM1855225", "GSM1855226", "GSM1855227", "GSM1855228", "GSM1855229", "GSM1855230", "GSM1855231", "GSM1855232", "GSM1855233", "GSM1855234", "GSM1855235", "GSM1855236", "GSM1855237", "GSM1855238"], "sample_count": 442, "group_sizes": null, "group_sizes_basis": null, "platform": "15048", "taxon": "Homo sapiens", "title": "KRAS mutation-associated gene expression, p53 and STK11 mutations, proliferation and immune surveillance in lung adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJEB23709", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJEB23709", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJEB23709", "version": null, "note": "Data can be obtained from the corresponding author when required.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data can be obtained from the corresponding author when required.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:46:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE117570 not downloaded", "asset:data:geo:GSE117570 licence not read", "asset:data:geo:GSE19188 not downloaded", "asset:data:geo:GSE19188 licence not read", "asset:data:geo:GSE30219 not downloaded", "asset:data:geo:GSE30219 licence not read", "asset:data:geo:GSE31547 not downloaded", "asset:data:geo:GSE31547 licence not read", "asset:data:geo:GSE37745 not downloaded", "asset:data:geo:GSE37745 licence not read", "asset:data:geo:GSE41271 not downloaded", "asset:data:geo:GSE41271 licence not read", "asset:data:geo:GSE42127 not downloaded", "asset:data:geo:GSE42127 licence not read", "asset:data:geo:GSE72094 not downloaded", "asset:data:geo:GSE72094 licence not read", "asset:data:geo:PRJEB23709 not downloaded", "asset:data:geo:PRJEB23709 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We performed univariate cox regression on all lipid metabolism-related genes to evaluate their impacts on the prognosis of LUAD patients."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.7, "band": "medium", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE37745", "GSE19188", "GSE30219", "GSE31547", "GSE41271", "GSE42127", "GSE72094", "PRJEB23709", "GSE117570"], "resolved_accessions": ["GSE37745", "GSE19188", "GSE30219", "GSE31547", "GSE41271", "GSE42127", "GSE72094", "GSE117570"], "statements": ["Data can be obtained from the corresponding author when required."], "basis": "The paper names GSE37745, GSE19188, GSE30219, GSE31547, GSE41271, GSE42127, GSE72094, GSE117570 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:37874388", "data:geo:GSE117570"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE117570"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:56:56Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10746, "completion_tokens": 1747, "cached_tokens": 0}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37874388", "type": "paper", "label": "pmid:37874388"}, {"id": "source:pmid:37874388", "type": "manuscript", "label": "PMID 37874388 full text"}, {"id": "data:geo:GSE117570", "type": "dataset", "label": "GEO GSE117570"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37874388", "type": "paper", "label": "pmid:37874388"}, {"id": "source:pmid:37874388", "type": "manuscript", "label": "PMID 37874388 full text"}, {"id": "data:geo:GSE117570", "type": "dataset", "label": "GEO GSE117570"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37874388", "type": "extraction", "used": ["source:pmid:37874388"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE117570", "type": "accession_resolution", "used": ["data:geo:GSE117570"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:37874388", "parent_hash": "sha256:fa3d39ab9768c15b1200472b95d5acbe62cddab69f950c6cfdc253e44687d333", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE117570 licence not read", "asset:data:geo:GSE117570 not downloaded", "asset:data:geo:GSE19188 licence not read", "asset:data:geo:GSE19188 not downloaded", "asset:data:geo:GSE30219 licence not read", "asset:data:geo:GSE30219 not downloaded", "asset:data:geo:GSE31547 licence not read", "asset:data:geo:GSE31547 not downloaded", "asset:data:geo:GSE37745 licence not read", "asset:data:geo:GSE37745 not downloaded", "asset:data:geo:GSE41271 licence not read", "asset:data:geo:GSE41271 not downloaded", "asset:data:geo:GSE42127 licence not read", "asset:data:geo:GSE42127 not downloaded", "asset:data:geo:GSE72094 licence not read", "asset:data:geo:GSE72094 not downloaded", "asset:data:geo:PRJEB23709 licence not read", "asset:data:geo:PRJEB23709 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ys including clone formation, EDU assays and flow cytometry were implemented to explore the phenotype al"], "order_basis": "paper_text_order:1192", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["plore the phenotype alteration caused by the knockdown of PTDSS1, which is one of key gene in risk", "Methods Cell culture and cell transfection Two cell lines of LUAD were used in this stu", "bserve the morphology of the cells. For cell transfection, A549 and NCI-H1975 were transfected with PT", "r cell transfection, A549 and NCI-H1975 were transfected with PTDSS1 knockdown siRNA. We used the 6-w"], "order_basis": "paper_text_order:1274", "id": "assay:2"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["re model. RESULTS: We analyzed both bulk and single-cell RNA sequencing data to establish and validate a risk score"], "order_basis": "paper_text_order:1376", "id": "assay:3"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["iferation of the cells was weakened, and the apoptosis of the cells was increased. CONCLUSION: Our", "owed that PTDSS1 regulated proliferation and apoptosis of LUAD cells."], "order_basis": "paper_text_order:1985", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Biosciences (Suzhou, China). The cells were cultured in complete medium, which consisted of 90% DMEM", "es of LUAD were used in this study. Both the A549 and NCI-H1975 were brought from Cyagen Biosc", "phology of the cells. For cell transfection, A549 and NCI-H1975 were transfected with PTDSS1 k"], "order_basis": "paper_text_order:2464", "id": "assay:5"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We performed univariate cox regression on all lipid metabolism-related genes to evaluate their impacts on the prognosis of LUAD patients."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T04:15:43+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}