{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39391517", "kind": "science-record", "revision": 4, "content_hash": "sha256:6a2207d7b30986857840f1e5d4cc47077030b48158a6b14fd82c3cb36523f4ed", "created_at": "2026-11-01T20:29:37Z", "updated_at": "2026-11-01T22:55:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Enhanced prognostic signature for lung adenocarcinoma through integration of adjacent normal and tumor gene expressions.", "doi": "10.1016/j.heliyon.2024.e38527", "pmid": "39391517", "authors": ["Mingyue Hao", "Dandan Li", "Weihao Chen", "Ming Xiong", "Xinkun Wang", "Yuanyuan Qiao", "Wei Ma"], "journal": "Heliyon", "year": 2024, "abstract": "Background: Cancer prognosis-related signatures have traditionally been constructed based on gene expression profiles derived from tumor or normal tissues. However, the potential benefits of incorporating gene expression profiles from both tumor and normal tissues to improve signature performance have not been explored.\nMethods: In this study, we developed three prognostic models for lung adenocarcinoma (LUAD) using gene expression profiles from tumor tissues, normal tissues, and a combination (COM) of both, sourced from The Cancer Genome Atlas (TCGA). To ensure comparability, the same workflow was followed for all three models.\nResults: When applied to the TCGA LUAD dataset, the tumor-derived model exhibited the best overall performance, except in calibration analysis, where the normal-derived model performed better. The COM-derived model demonstrated intermediate performance. Validation on three independent test datasets revealed that the COM-derived model showed the best performance, while the normal-derived model showed the worst. In overall survival (OS) analysis, the low-risk group defined by the COM-derived model consistently exhibited longer mean survival times. The tumor-derived model did not consistently show this trend, and the normal-derived model produced opposite results. In discrimination analysis, no significant differences were observed. The COM-derived model demonstrated good discrimination ability for short periods, while the tumor-derived model performed better for longer periods. In calibration analysis, both the COM and tumor-derived models had similar absolute prediction errors, which were better than those of the normal-derived model. However, the tumor-derived model tended to underestimate survival rates. The clinical feature analysis and validation in GSE229705 indicate that the risk score (RS) from the COM model is the most clinically significant. These results demonstrate that the COM model's RS aligns more closely with clinical data, maintaining stable performance and the strongest generalizability.\nConclusions: Overall, the COM-derived model demonstrated the best generalization ability. The superior performance of the tumor-derived model in the TCGA LUAD dataset might be due to overfitting. Our results suggest that appropriate combinations of gene expression data from tumor and normal tissues can enhance the predictive power of prognostic signatures.", "claims": [{"id": "claim-method", "statement": "Univariable Cox regression analysis was performed for each gene to explore OS-related genes in both tumor and normal samples. To reduce dimensionality and select genes from the candidate gene set, Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression was employed. Stepwise regression was then used to build the OS prognosis models. Survival curve analysis was calculated using the Kaplan–Meier (K-M) method, and differences between survival curves were assessed using the log-rank test via the survival R package. For discrimination analysis, the time-dependent receiver operating characteristic curve (timeROC) was employed to evaluate the discrimination of models using the timeROC R package. Calibration analysis was performed using the survival R package, evaluating calibration performance based on the absolute difference values between predicted and calculated survival rates.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39391517", "locator": "sections[4] \"Gene selection model construction\" paragraph 2", "quote": "Univariable Cox regression analysis was performed for each gene to explore OS-related genes in both tumor and normal samples."}, {"asset": "source:pmid:39391517", "locator": "sections[4] \"Gene selection model construction\" paragraph 2", "quote": "To reduce dimensionality and select genes from the candidate gene set, Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression was employed."}, {"asset": "source:pmid:39391517", "locator": "sections[4] \"Gene selection model construction\" paragraph 2", "quote": "Stepwise regression was then used to build the OS prognosis models."}, {"asset": "source:pmid:39391517", "locator": "sections[5] \"Model validation\" paragraph 2", "quote": "Survival curve analysis was calculated using the Kaplan–Meier (K-M) method, and differences between survival curves were assessed using the log-rank test via the survival R package."}, {"asset": "source:pmid:39391517", "locator": "sections[5] \"Model validation\" paragraph 2", "quote": "For discrimination analysis, the time-dependent receiver operating characteristic curve (timeROC) was employed to evaluate the discrimination of models using the timeROC R package."}, {"asset": "source:pmid:39391517", "locator": "sections[5] \"Model validation\" paragraph 2", "quote": "Calibration analysis was performed using the survival R package, evaluating calibration performance based on the absolute difference values between predicted and calculated survival rates."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data used in this study were open access.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39391517", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "All data used in this study were open access."}], "state": "complete"}, {"id": "claim-target-result", "statement": "For the COM model, a 7-gene-based model was built, including 6 genes from SUM (APOD, FUT2, TUBE1, C1orf105, HIST1H3I, and OPALIN) 1 gene from LogTN (COX6B2) (Fig. 2A).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39391517", "locator": "sections[10] \"Construction of three prognosis models based on candidate genes of tumor, normal, and COM in TCGA LUAD\" paragraph 2", "quote": "For the COM model, a 7-gene-based model was built, including 6 genes from SUM (APOD, FUT2, TUBE1, C1orf105, HIST1H3I, and OPALIN) 1 gene from LogTN (COX6B2) (Fig. 2A)."}, {"asset": "source:pmid:39391517", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Overall, the COM-derived model demonstrated the best generalization ability."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "For the COM model, a 7-gene-based model was built, including 6 genes from SUM (APOD, FUT2, TUBE1, C1orf105, HIST1H3I, and OPALIN) 1 gene from LogTN (COX6B2) (Fig. 2A).", "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:39391517"], "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:GSE102287"], "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:GSE102287"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39391517", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e38527", "sha256": "sha256:baffbc5b652aa7576a55d3ec59f46226fbac118fed8226db3af2ae0f68017578", "bytes": 45591, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2024.e38527", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11466592", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102287", "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=GSE102287", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102287", "version": null, "note": "All data used in this study were open access.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data used in this study were open access.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2718949", "GSM2718950", "GSM2718951", "GSM2718952", "GSM2718953", "GSM2718954", "GSM2718955", "GSM2718956", "GSM2718957", "GSM2718958", "GSM2718959", "GSM2718960", "GSM2718961", "GSM2718962", "GSM2718963", "GSM2718964", "GSM2718965", "GSM2718966", "GSM2718967", "GSM2718968", "GSM2718969", "GSM2718970", "GSM2718971", "GSM2718972", "GSM2718973", "GSM2718974", "GSM2718975", "GSM2718976", "GSM2718977", "GSM2718978", "GSM2718979", "GSM2718980", "GSM2718981", "GSM2718982", "GSM2718983", "GSM2718984", "GSM2718985", "GSM2718986", "GSM2718987", "GSM2718988", "GSM2718989", "GSM2718990", "GSM2718991", "GSM2718992", "GSM2718993", "GSM2718994", "GSM2718995", "GSM2718996", "GSM2718997", "GSM2718998", "GSM2718999", "GSM2719000", "GSM2719001", "GSM2719002", "GSM2719003", "GSM2719004", "GSM2719005", "GSM2719006", "GSM2719007", "GSM2719008", "GSM2719009", "GSM2719010", "GSM2719011", "GSM2719012", "GSM2719013", "GSM2719014", "GSM2732934", "GSM2732935", "GSM2732936", "GSM2732937", "GSM2732938", "GSM2732939", "GSM2732940", "GSM2732941", "GSM2732942", "GSM2732943", "GSM2732944", "GSM2732945", "GSM2732946", "GSM2732947", "GSM2732948", "GSM2732949", "GSM2732950", "GSM2732951", "GSM2732952", "GSM2732953", "GSM2732954", "GSM2732955", "GSM2732956", "GSM2732957", "GSM2732958", "GSM2732959", "GSM2732960", "GSM2732961", "GSM2732962", "GSM2732963", "GSM2732964", "GSM2732965", "GSM2732966", "GSM2732967", "GSM2732968", "GSM2732969", "GSM2732970", "GSM2732971", "GSM2732972", "GSM2732973", "GSM2732974", "GSM2732975", "GSM2732976", "GSM2732977", "GSM2732978", "GSM2732979", "GSM2732980", "GSM2732981", "GSM2732982", "GSM2732983", "GSM2732984", "GSM2732985", "GSM2732986", "GSM2732987", "GSM2732988", "GSM2732989", "GSM2732990", "GSM2732991", "GSM2732992", "GSM2732993", "GSM2732994", "GSM2732995", "GSM2732996", "GSM2732997", "GSM2732998", "GSM2732999", "GSM2733000", "GSM2733001", "GSM2733002", "GSM2733003", "GSM2733004", "GSM2733005", "GSM2733006", "GSM2733007", "GSM2733008", "GSM2733009", "GSM2733010", "GSM2733011", "GSM2733012", "GSM2733013", "GSM2733014", "GSM2733015", "GSM2733016", "GSM2733017", "GSM2733018", "GSM2733019", "GSM2733020", "GSM2733021", "GSM2733022", "GSM2733023", "GSM2733024", "GSM2733025", "GSM2733026", "GSM2733027", "GSM2733028", "GSM2733029", "GSM2733030", "GSM2733031", "GSM2733032", "GSM2733033", "GSM2733034", "GSM2733035", "GSM2733036", "GSM2733037", "GSM2733038", "GSM2733039", "GSM2733040", "GSM2733041", "GSM2733042", "GSM2733043", "GSM2733044", "GSM2733045", "GSM2733046", "GSM2733047", "GSM2733048", "GSM2733049", "GSM2733050", "GSM2733051", "GSM2733052", "GSM2733053", "GSM2733054", "GSM2733055", "GSM2733056", "GSM2733057", "GSM2733058", "GSM2733059", "GSM2733060", "GSM2733061", "GSM2733062", "GSM2733063", "GSM2733064", "GSM2733065", "GSM2733066", "GSM2733067", "GSM2733068", "GSM2733069", "GSM2733070", "GSM2733071", "GSM2733072", "GSM2733073", "GSM2733074", "GSM2733075", "GSM2733076", "GSM2733077", "GSM2733078", "GSM2733079", "GSM2733080", "GSM2733081", "GSM2733082", "GSM2733083", "GSM2733084", "GSM2733085", "GSM2733086", "GSM2733087", "GSM2733088", "GSM2733089", "GSM2733090", "GSM2733091", "GSM2733092", "GSM2733093", "GSM2733094", "GSM2733095", "GSM2733096", "GSM2733097", "GSM2733098", "GSM2733099", "GSM2733100", "GSM2733101", "GSM2733102", "GSM2733103", "GSM2733104", "GSM2733105", "GSM2733106", "GSM2733107", "GSM2733108", "GSM2733109", "GSM2733110", "GSM2733111", "GSM2733112"], "sample_count": 245, "group_sizes": null, "group_sizes_basis": null, "platform": "570;23871", "taxon": "Homo sapiens", "title": "Gene and microRNA expression data from African Americans and European Americans with 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:GSE229705", "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=GSE229705", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE229705", "version": null, "note": "All data used in this study were open access.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data used in this study were open access.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM7173464", "GSM7173465", "GSM7173466", "GSM7173467", "GSM7173468", "GSM7173469", "GSM7173470", "GSM7173471", "GSM7173472", "GSM7173473", "GSM7173474", "GSM7173475", "GSM7173476", "GSM7173477", "GSM7173478", "GSM7173479", "GSM7173480", "GSM7173481", "GSM7173482", "GSM7173483", "GSM7173484", "GSM7173485", "GSM7173486", "GSM7173487", "GSM7173488", "GSM7173489", "GSM7173490", "GSM7173491", "GSM7173492", "GSM7173493", "GSM7173494", "GSM7173495", "GSM7173496", "GSM7173497", "GSM7173498", "GSM7173499", "GSM7173500", "GSM7173501", "GSM7173502", "GSM7173503", "GSM7173504", "GSM7173505", "GSM7173506", "GSM7173507", "GSM7173508", "GSM7173509", "GSM7173510", "GSM7173511", "GSM7173512", "GSM7173513", "GSM7173514", "GSM7173515", "GSM7173516", "GSM7173517", "GSM7173518", "GSM7173519", "GSM7173520", "GSM7173521", "GSM7173522", "GSM7173523", "GSM7173524", "GSM7173525", "GSM7173526", "GSM7173527", "GSM7173528", "GSM7173529", "GSM7173530", "GSM7173531", "GSM7173532", "GSM7173533", "GSM7173534", "GSM7173535", "GSM7173536", "GSM7173537", "GSM7173538", "GSM7173539", "GSM7173540", "GSM7173541", "GSM7173542", "GSM7173543", "GSM7173544", "GSM7173545", "GSM7173546", "GSM7173547", "GSM7173548", "GSM7173549", "GSM7173550", "GSM7173551", "GSM7173552", "GSM7173553", "GSM7173554", "GSM7173555", "GSM7173556", "GSM7173557", "GSM7173558", "GSM7173559", "GSM7173560", "GSM7173561", "GSM7173562", "GSM7173563", "GSM7173564", "GSM7173565", "GSM7173566", "GSM7173567", "GSM7173568", "GSM7173569", "GSM7173570", "GSM7173571", "GSM7173572", "GSM7173573", "GSM7173574", "GSM7173575", "GSM7173576", "GSM7173577", "GSM7173578", "GSM7173579", "GSM7173580", "GSM7173581", "GSM7173582", "GSM7173583", "GSM7173584", "GSM7173585", "GSM7173586", "GSM7173587", "GSM7173588", "GSM7173589", "GSM7173590", "GSM7173591", "GSM7173592", "GSM7173593", "GSM7173594", "GSM7173595", "GSM7173596", "GSM7173597", "GSM7173598", "GSM7173599", "GSM7173600", "GSM7173601", "GSM7173602", "GSM7173603", "GSM7173604", "GSM7173605", "GSM7173606", "GSM7173607", "GSM7173608", "GSM7173609", "GSM7173610", "GSM7173611", "GSM7173612", "GSM7173613", "GSM7173614", "GSM7173615", "GSM7173616", "GSM7173617", "GSM7173618", "GSM7173619", "GSM7173620", "GSM7173621", "GSM7173622", "GSM7173623", "GSM7173624", "GSM7173625", "GSM7173626", "GSM7173627", "GSM7173628", "GSM7173629", "GSM7173630", "GSM7173631", "GSM7173632", "GSM7173633", "GSM7173634", "GSM7173635", "GSM7173636", "GSM7173637", "GSM7173638", "GSM7173639", "GSM7173640", "GSM7173641", "GSM7173642", "GSM7173643", "GSM7173644", "GSM7173645", "GSM7173646", "GSM7173647", "GSM7173648", "GSM7173649", "GSM7173650", "GSM7173651", "GSM7173652", "GSM7173653", "GSM7173654", "GSM7173655", "GSM7173656", "GSM7173657", "GSM7173658", "GSM7173659", "GSM7173660", "GSM7173661", "GSM7173662", "GSM7173663", "GSM7173664", "GSM7173665", "GSM7173666", "GSM7173667", "GSM7173668", "GSM7173669", "GSM7173670", "GSM7173671", "GSM7173672", "GSM7173673", "GSM7173674", "GSM7173675", "GSM7173676", "GSM7173677", "GSM7173678", "GSM7173679", "GSM7173680", "GSM7173681", "GSM7173682", "GSM7173683", "GSM7173684", "GSM7173685", "GSM7173686", "GSM7173687", "GSM7173688", "GSM7173689", "GSM7173690", "GSM7173691", "GSM7173692", "GSM7173693", "GSM7173694", "GSM7173695", "GSM7173696", "GSM7173697", "GSM7173698", "GSM7173699", "GSM7173700", "GSM7173701", "GSM7173702", "GSM7173703", "GSM7173704", "GSM7173705", "GSM7173706", "GSM7173707", "GSM7173708", "GSM7173709"], "sample_count": 246, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Tumor-adjacent lung transcriptome as a predictor of recurrence in early-stage lung adenocarcinoma [bulk RNA-seq]", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE31210", "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=GSE31210", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31210", "version": null, "note": "All data used in this study were open access.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data used in this study were open access.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM773540", "GSM773541", "GSM773542", "GSM773543", "GSM773544", "GSM773545", "GSM773546", "GSM773547", "GSM773548", "GSM773549", "GSM773550", "GSM773551", "GSM773552", "GSM773553", "GSM773554", "GSM773555", "GSM773556", "GSM773557", "GSM773558", "GSM773559", "GSM773560", "GSM773561", "GSM773562", "GSM773563", "GSM773564", "GSM773565", "GSM773566", "GSM773567", "GSM773568", "GSM773569", "GSM773570", "GSM773571", "GSM773572", "GSM773573", "GSM773574", "GSM773575", "GSM773576", "GSM773577", "GSM773578", "GSM773579", "GSM773580", "GSM773581", "GSM773582", "GSM773583", "GSM773584", "GSM773585", "GSM773586", "GSM773587", "GSM773588", "GSM773589", "GSM773590", "GSM773591", "GSM773592", "GSM773593", "GSM773594", "GSM773595", "GSM773596", "GSM773597", "GSM773598", "GSM773599", "GSM773600", "GSM773601", "GSM773602", "GSM773603", "GSM773604", "GSM773605", "GSM773606", "GSM773607", "GSM773608", "GSM773609", "GSM773610", "GSM773611", "GSM773612", "GSM773613", "GSM773614", "GSM773615", "GSM773616", "GSM773617", "GSM773618", "GSM773619", "GSM773620", "GSM773621", "GSM773622", "GSM773623", "GSM773624", "GSM773625", "GSM773626", "GSM773627", "GSM773628", "GSM773629", "GSM773630", "GSM773631", "GSM773632", "GSM773633", "GSM773634", "GSM773635", "GSM773636", "GSM773637", "GSM773638", "GSM773639", "GSM773640", "GSM773641", "GSM773642", "GSM773643", "GSM773644", "GSM773645", "GSM773646", "GSM773647", "GSM773648", "GSM773649", "GSM773650", "GSM773651", "GSM773652", "GSM773653", "GSM773654", "GSM773655", "GSM773656", "GSM773657", "GSM773658", "GSM773659", "GSM773660", "GSM773661", "GSM773662", "GSM773663", "GSM773664", "GSM773665", "GSM773666", "GSM773667", "GSM773668", "GSM773669", "GSM773670", "GSM773671", "GSM773672", "GSM773673", "GSM773674", "GSM773675", "GSM773676", "GSM773677", "GSM773678", "GSM773679", "GSM773680", "GSM773681", "GSM773682", "GSM773683", "GSM773684", "GSM773685", "GSM773686", "GSM773687", "GSM773688", "GSM773689", "GSM773690", "GSM773691", "GSM773692", "GSM773693", "GSM773694", "GSM773695", "GSM773696", "GSM773697", "GSM773698", "GSM773699", "GSM773700", "GSM773701", "GSM773702", "GSM773703", "GSM773704", "GSM773705", "GSM773706", "GSM773707", "GSM773708", "GSM773709", "GSM773710", "GSM773711", "GSM773712", "GSM773713", "GSM773714", "GSM773715", "GSM773716", "GSM773717", "GSM773718", "GSM773719", "GSM773720", "GSM773721", "GSM773722", "GSM773723", "GSM773724", "GSM773725", "GSM773726", "GSM773727", "GSM773728", "GSM773729", "GSM773730", "GSM773731", "GSM773732", "GSM773733", "GSM773734", "GSM773735", "GSM773736", "GSM773737", "GSM773738", "GSM773739", "GSM773740", "GSM773741", "GSM773742", "GSM773743", "GSM773744", "GSM773745", "GSM773746", "GSM773747", "GSM773748", "GSM773749", "GSM773750", "GSM773751", "GSM773752", "GSM773753", "GSM773754", "GSM773755", "GSM773756", "GSM773757", "GSM773758", "GSM773759", "GSM773760", "GSM773761", "GSM773762", "GSM773763", "GSM773764", "GSM773765", "GSM773766", "GSM773767", "GSM773768", "GSM773769", "GSM773770", "GSM773771", "GSM773772", "GSM773773", "GSM773774", "GSM773775", "GSM773776", "GSM773777", "GSM773778", "GSM773779", "GSM773780", "GSM773781", "GSM773782", "GSM773783", "GSM773784", "GSM773785"], "sample_count": 246, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data for pathological stage I-II lung adenocarcinomas", "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:GSE81089", "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=GSE81089", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE81089", "version": null, "note": "All data used in this study were open access.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data used in this study were open access.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2142443", "GSM2142444", "GSM2142445", "GSM2142446", "GSM2142447", "GSM2142448", "GSM2142449", "GSM2142450", "GSM2142451", "GSM2142452", "GSM2142453", "GSM2142454", "GSM2142455", "GSM2142456", "GSM2142457", "GSM2142458", "GSM2142459", "GSM2142460", "GSM2142461", "GSM2142462", "GSM2142463", "GSM2142464", "GSM2142465", "GSM2142466", "GSM2142467", "GSM2142468", "GSM2142469", "GSM2142470", "GSM2142471", "GSM2142472", "GSM2142473", "GSM2142474", "GSM2142475", "GSM2142476", "GSM2142477", "GSM2142478", "GSM2142479", "GSM2142480", "GSM2142481", "GSM2142482", "GSM2142483", "GSM2142484", "GSM2142485", "GSM2142486", "GSM2142487", "GSM2142488", "GSM2142489", "GSM2142490", "GSM2142491", "GSM2142492", "GSM2142493", "GSM2142494", "GSM2142495", "GSM2142496", "GSM2142497", "GSM2142498", "GSM2142499", "GSM2142500", "GSM2142501", "GSM2142502", "GSM2142503", "GSM2142504", "GSM2142505", "GSM2142506", "GSM2142507", "GSM2142508", "GSM2142509", "GSM2142510", "GSM2142511", "GSM2142512", "GSM2142513", "GSM2142514", "GSM2142515", "GSM2142516", "GSM2142517", "GSM2142518", "GSM2142519", "GSM2142520", "GSM2142521", "GSM2142522", "GSM2142523", "GSM2142524", "GSM2142525", "GSM2142526", "GSM2142527", "GSM2142528", "GSM2142529", "GSM2142530", "GSM2142531", "GSM2142532", "GSM2142533", "GSM2142534", "GSM2142535", "GSM2142536", "GSM2142537", "GSM2142538", "GSM2142539", "GSM2142540", "GSM2142541", "GSM2142542", "GSM2142543", "GSM2142544", "GSM2142545", "GSM2142546", "GSM2142547", "GSM2142548", "GSM2142549", "GSM2142550", "GSM2142551", "GSM2142552", "GSM2142553", "GSM2142554", "GSM2142555", "GSM2142556", "GSM2142557", "GSM2142558", "GSM2142559", "GSM2142560", "GSM2142561", "GSM2142562", "GSM2142563", "GSM2142564", "GSM2142565", "GSM2142566", "GSM2142567", "GSM2142568", "GSM2142569", "GSM2142570", "GSM2142571", "GSM2142572", "GSM2142573", "GSM2142574", "GSM2142575", "GSM2142576", "GSM2142577", "GSM2142578", "GSM2142579", "GSM2142580", "GSM2142581", "GSM2142582", "GSM2142583", "GSM2142584", "GSM2142585", "GSM2142586", "GSM2142587", "GSM2142588", "GSM2142589", "GSM2142590", "GSM2142591", "GSM2142592", "GSM2142593", "GSM2142594", "GSM2142595", "GSM2142596", "GSM2142597", "GSM2142598", "GSM2142599", "GSM2142600", "GSM2142601", "GSM2142602", "GSM2142603", "GSM2142604", "GSM2142605", "GSM2142606", "GSM2142607", "GSM2142608", "GSM2142609", "GSM2142610", "GSM2142611", "GSM2142612", "GSM2142613", "GSM2142614", "GSM2142615", "GSM2142616", "GSM2142617", "GSM2142618", "GSM2142619", "GSM2142620", "GSM2142621", "GSM2142622", "GSM2142623", "GSM2142624", "GSM2142625", "GSM2142626", "GSM2142627", "GSM2142628", "GSM2142629", "GSM2142630", "GSM2142631", "GSM2142632", "GSM2142633", "GSM2142634", "GSM2142635", "GSM2142636", "GSM2142637", "GSM2142638", "GSM2142639", "GSM2142640", "GSM2142641", "GSM2142642", "GSM2142643", "GSM2142644", "GSM2142645", "GSM2142646", "GSM2142647", "GSM2142648", "GSM2142649", "GSM2142650", "GSM2142651", "GSM2142652", "GSM2142653", "GSM2142654", "GSM2142655", "GSM2142656", "GSM2142657", "GSM2142658", "GSM2142659", "GSM2142660"], "sample_count": 218, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "Next Generation Sequencing (RNAseq) of non-small cell lung cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE102287 not downloaded", "asset:data:geo:GSE102287 licence not read", "asset:data:geo:GSE229705 not downloaded", "asset:data:geo:GSE229705 licence not read", "asset:data:geo:GSE31210 not downloaded", "asset:data:geo:GSE31210 licence not read", "asset:data:geo:GSE81089 not downloaded", "asset:data:geo:GSE81089 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": "reordered", "quote": "Univariable Cox regression analysis was performed for each gene to explore OS-related genes in both tumor and normal samples. To reduce dimensionality and select genes from the candidate gene set, Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression was employed. Stepwise regression was then used to build the OS prognosis models. Survival curve analysis was calculated using the Kaplan–Meier (K-M) method, and differences between survival curves were assessed using the log-rank test via the survival R package. For discrimination analysis, the time-dependent receiver operating characteristic curve (timeROC) was employed to evaluate the discrimination of models using the timeROC R package. Calibration analysis was performed using the survival R package, evaluating calibration performance based on the absolute difference values between predicted and calculated survival rates."}}, {"id": "method-2", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Student's t-test"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}, {"id": "method-5", "family": "contingency_analysis", "specific": "fisher_exact", "label": "Categorical (contingency table) analysis", "dsl_operations": ["contingency_table", "chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Fisher's exact"}}], "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": ["GSE81089", "GSE102287", "GSE31210", "GSE229705"], "resolved_accessions": ["GSE81089", "GSE102287", "GSE31210", "GSE229705"], "statements": ["All data used in this study were open access."], "basis": "The paper names GSE81089, GSE102287, GSE31210, GSE229705 in Gene Expression Omnibus (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:39391517", "data:geo:GSE102287"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102287"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:34:50Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12552, "completion_tokens": 2682, "cached_tokens": 256}}, "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:39391517", "type": "paper", "label": "pmid:39391517"}, {"id": "source:pmid:39391517", "type": "manuscript", "label": "PMID 39391517 full text"}, {"id": "data:geo:GSE102287", "type": "dataset", "label": "GEO GSE102287"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39391517", "type": "paper", "label": "pmid:39391517"}, {"id": "source:pmid:39391517", "type": "manuscript", "label": "PMID 39391517 full text"}, {"id": "data:geo:GSE102287", "type": "dataset", "label": "GEO GSE102287"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39391517", "type": "extraction", "used": ["source:pmid:39391517"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102287", "type": "accession_resolution", "used": ["data:geo:GSE102287"], "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:39391517", "parent_hash": "sha256:4601634fd0d3edc3c22cb86d19c5325ee0a23573d82d7adee117b82e3b3c8089", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE102287 licence not read", "asset:data:geo:GSE102287 not downloaded", "asset:data:geo:GSE229705 licence not read", "asset:data:geo:GSE229705 not downloaded", "asset:data:geo:GSE31210 licence not read", "asset:data:geo:GSE31210 not downloaded", "asset:data:geo:GSE81089 licence not read", "asset:data:geo:GSE81089 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["Univariable Cox regression analysis was performed for each gene to explore OS-related genes in both tumor and normal samples. To reduce dimensionality and select genes from the candidate gene set, Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression was employed. Stepwise regression was then used to build the OS prognosis models. Survival curve analysis was calculated using the Kaplan–Meier (K-M) method, and differences between survival curves were assessed using the log-rank test via the survival R package. For discrimination analysis, the time-dependent receiver operating characteristic curve (timeROC) was employed to evaluate the discrimination of models using the timeROC R package. Calibration analysis was performed using the survival R package, evaluating calibration performance based on the absolute difference values between predicted and calculated survival rates."], "order_basis": "analysis_only", "id": "assay:1"}]},"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":"2026-11-04T00:41:13+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}}}