{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39033204", "kind": "science-record", "revision": 3, "content_hash": "sha256:b6324d7041f76242a9e11839adc9ba80af1a6d5dc14473b5726b6032510f2a6c", "created_at": "2026-11-01T20:29:06Z", "updated_at": "2026-11-01T22:12:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Angiogenesis related genes based prognostic model of glioma patients developed by multi-omics approach.", "doi": "10.1007/s12672-024-01126-6", "pmid": "39033204", "authors": ["Zhimin Liu", "Hongjun Fan", "XuKai Liu", "Chao Liu"], "journal": "Discover oncology", "year": 2024, "abstract": "INTRODUCTION: Glioma, particularly glioblastoma (GBM), is a highly malignant brain tumor with poor prognosis despite current therapeutic approaches. The tumor microenvironment (TME), plays a crucial role in glioma progression by promoting invasion and drug resistance. Angiogenesis, the formation of new blood vessels, is a tightly regulated process involving endothelial cell activation, proliferation, and migration. In cancer, angiogenesis becomes dysregulated, leading to excessive blood vessel formation.\nMETHODS: We enrolled bulk data of TCGA-LGG/GBM, CGGA-693, and CGGA-325 cohorts, scRNA data of GSE162631, GSE84465, and GSE138794 cohorts. Identification of malignant cells was conducted by \"copycat\" R package. The \"AUCell\" R package scored the activity of target gene set of each single cell. Consensus clustering was applied using the \"ConsensusClusterPlus\" R package, while tumor-infiltrating immune cells were determined using \"IOBR\" R package. To construct a prognostic model, we used LASSO and multiCOX algorithms based on the expression levels of the 15 hub genes, the efficacy of which was verified by KM and ROC analysis.\nRESULTS: We identified 4 different malignant cell subclusters in glioma and disclosed their distinct gene expression patterns and interactions within TME. We identified differentially expressed immune-related genes (DE-ARGs) in glioma and found 15 genes that were specifically expressed in the malignant glioma cell populations. Glioma cells with higher expression of these DE-ARGs were associated with gliogenesis, glial cell development, and vasculature development. We found that tumor-infiltrating monocytes were the main interacting cell type within glioma TME. Using the expression patterns of the 15 screened DE-ARGs, we categorized glioma samples into 2 molecular clusters with distinct immune features, suggesting a possible relationship between angiogenesis and immune activation and recruitment. We constructed a prognostic model based on the expression levels of the 15 DE-ARGs and evaluated its predictive ability for glioma patient outcomes, which displayed exceedingly high efficacy.\nCONCLUSION: We characterized different malignant cell subclusters in glioma and investigate their gene expression patterns and interactions within TME. We constructed a prognostic model based on the expression levels of the 15 DE-ARGs and evaluated its predictive ability for glioma patient outcomes, which displayed exceedingly high efficacy.", "claims": [{"id": "claim-method", "statement": "Based on 15 hub genes, a prognostic model was constructed using LASSO and multiCOX.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39033204", "locator": "sections[9] \"Prognosis model construction and nomogram model establishment\" paragraph 2", "quote": "Based on 15 hub genes, a prognostic model was constructed using LASSO and multiCOX."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data could be obtained from TCGA database,or coresponding author after the requestion.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39033204", "locator": "sections[21] \"Data availability\" paragraph 2", "quote": "The data could be obtained from TCGA database,or coresponding author after the requestion."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A LASSO and multiCOX prognostic model based on 15 DE-ARGs identified inferior outcomes for patients with higher risk scores across all three cohorts and achieved AUC values above 0.9 at 1 and 3 years postoperatively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39033204", "locator": "sections[17] \"Prognostic model construction and nomogram establishment\" paragraph 2", "quote": "We found that a unanimous inferior clinical outcome of glioma patients of relatively higher risk value across all 3 cohorts, which were further support by an exceedingly satisfactory AUC value above 0.9 at 1 year and 3 years post-operative time points (Fig. 9c)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A LASSO and multiCOX prognostic model based on 15 DE-ARGs identified inferior outcomes for patients with higher risk scores across all three cohorts and achieved AUC values above 0.9 at 1 and 3 years postoperatively.", "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:39033204"], "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:GSE138794"], "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:GSE138794"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39033204", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-024-01126-6", "sha256": 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"access_route": "GEO accession URL", "access_statement_verbatim": "The data could be obtained from TCGA database,or coresponding author after the requestion.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4119513", "GSM4119514", "GSM4119515", "GSM4119516", "GSM4119517", "GSM4119518", "GSM4119519", "GSM4119520", "GSM4119521", "GSM4119522", "GSM4119523", "GSM4119524", "GSM4119525", "GSM4119526", "GSM4119527", "GSM4119528", "GSM4119529", "GSM4119530", "GSM4119531", "GSM4119532", "GSM4119533", "GSM4119534", "GSM4119535", "GSM4119536", "GSM4119537", "GSM4119538", "GSM4119539", "GSM4658373"], "sample_count": 28, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "A single cell atlas of human glioma", "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:GSE162631", "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=GSE162631", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE162631", "version": null, "note": "The data could be obtained from TCGA database,or coresponding author after the requestion.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data could be obtained from TCGA database,or coresponding author after the requestion.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4955731", "GSM4955732", "GSM4955733", "GSM4955734", "GSM4955735", "GSM4955736", "GSM4955737", "GSM4955738"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Single cell RNA-seq of brain glioblastoma samples", 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"GSM2244161", "GSM2244162", "GSM2244163", "GSM2244164", "GSM2244165", "GSM2244166", "GSM2244167", "GSM2244168", "GSM2244169", "GSM2244170", "GSM2244171", "GSM2244172", "GSM2244173", "GSM2244174", "GSM2244175", "GSM2244176", "GSM2244177", "GSM2244178", "GSM2244179", "GSM2244180", "GSM2244181", "GSM2244182", "GSM2244183", "GSM2244184", "GSM2244185", "GSM2244186", "GSM2244187", "GSM2244188", "GSM2244189", "GSM2244190", "GSM2244191", "GSM2244192", "GSM2244193", "GSM2244194", "GSM2244195", "GSM2244196", "GSM2244197", "GSM2244198", "GSM2244199", "GSM2244200", "GSM2244201", "GSM2244202", "GSM2244203", "GSM2244204", "GSM2244205", "GSM2244206", "GSM2244207", "GSM2244208", "GSM2244209", "GSM2244210", "GSM2244211", "GSM2244212", "GSM2244213", "GSM2244214", "GSM2244215", "GSM2244216", "GSM2244217", "GSM2244218", "GSM2244219", "GSM2244220", "GSM2244221", "GSM2244222", "GSM2244223", "GSM2244224", "GSM2244225", "GSM2244226", "GSM2244227", "GSM2244228", "GSM2244229", "GSM2244230", "GSM2244231", "GSM2244232", "GSM2244233", "GSM2244234", "GSM2244235", "GSM2244236", "GSM2244237", "GSM2244238", "GSM2244239", "GSM2244240", "GSM2244241", "GSM2244242", "GSM2244243", "GSM2244244", "GSM2244245", "GSM2244246", "GSM2244247", "GSM2244248", "GSM2244249", "GSM2244250", "GSM2244251", "GSM2244252", "GSM2244253", "GSM2244254", "GSM2244255", "GSM2244256", "GSM2244257", "GSM2244258", "GSM2244259", "GSM2244260", "GSM2244261", "GSM2244262", "GSM2244263", "GSM2244264", "GSM2244265", "GSM2244266", "GSM2244267", "GSM2244268", "GSM2244269", "GSM2244270", "GSM2244271", "GSM2244272", "GSM2244273", "GSM2244274", "GSM2244275", "GSM2244276", "GSM2244277", "GSM2244278", "GSM2244279", "GSM2244280", "GSM2244281", "GSM2244282", "GSM2244283", "GSM2244284", "GSM2244285", "GSM2244286", "GSM2244287", "GSM2244288", "GSM2244289", "GSM2244290", "GSM2244291", "GSM2244292", "GSM2244293", "GSM2244294", "GSM2244295", "GSM2244296", "GSM2244297", "GSM2244298", "GSM2244299", "GSM2244300", "GSM2244301", "GSM2244302", "GSM2244303", "GSM2244304", "GSM2244305", "GSM2244306", "GSM2244307", "GSM2244308", "GSM2244309", "GSM2244310", "GSM2244311", "GSM2244312", "GSM2244313", "GSM2244314", "GSM2244315", "GSM2244316", "GSM2244317", "GSM2244318", "GSM2244319", "GSM2244320", "GSM2244321", "GSM2244322", "GSM2244323", "GSM2244324", "GSM2244325", "GSM2244326", "GSM2244327", "GSM2244328", "GSM2244329", "GSM2244330", "GSM2244331", "GSM2244332", "GSM2244333", "GSM2244334", "GSM2244335", "GSM2244336", "GSM2244337", "GSM2244338", "GSM2244339", "GSM2244340", "GSM2244341", "GSM2244342", "GSM2244343", "GSM2244344", "GSM2244345", "GSM2244346", "GSM2244347", "GSM2244348", "GSM2244349", "GSM2244350", "GSM2244351", "GSM2244352", "GSM2244353", "GSM2244354", "GSM2244355", "GSM2244356", "GSM2244357", "GSM2244358", "GSM2244359", "GSM2244360", "GSM2244361", "GSM2244362", "GSM2244363", "GSM2244364", "GSM2244365", "GSM2244366", "GSM2244367", "GSM2244368", "GSM2244369", "GSM2244370", "GSM2244371", "GSM2244372", "GSM2244373", "GSM2244374", "GSM2244375", "GSM2244376", "GSM2244377", "GSM2244378", "GSM2244379", "GSM2244380", "GSM2244381", "GSM2244382", "GSM2244383", "GSM2244384", "GSM2244385", "GSM2244386", "GSM2244387", "GSM2244388", "GSM2244389", "GSM2244390", "GSM2244391", "GSM2244392", "GSM2244393", "GSM2244394", "GSM2244395", "GSM2244396", "GSM2244397", "GSM2244398", "GSM2244399", "GSM2244400", "GSM2244401", "GSM2244402", "GSM2244403", "GSM2244404", "GSM2244405", "GSM2244406", "GSM2244407", "GSM2244408", "GSM2244409", "GSM2244410", "GSM2244411", "GSM2244412", "GSM2244413", "GSM2244414", "GSM2244415", "GSM2244416", "GSM2244417", "GSM2244418", "GSM2244419", "GSM2244420", "GSM2244421", "GSM2244422", "GSM2244423", "GSM2244424", "GSM2244425", "GSM2244426", "GSM2244427", "GSM2244428", "GSM2244429", "GSM2244430", "GSM2244431", "GSM2244432", "GSM2244433", "GSM2244434", "GSM2244435", "GSM2244436", "GSM2244437", "GSM2244438", "GSM2244439", "GSM2244440", "GSM2244441", "GSM2244442", "GSM2244443", "GSM2244444", "GSM2244445", "GSM2244446", "GSM2244447", "GSM2244448", "GSM2244449", "GSM2244450", "GSM2244451", "GSM2244452", "GSM2244453", "GSM2244454", "GSM2244455", "GSM2244456", "GSM2244457", "GSM2244458", "GSM2244459", "GSM2244460", "GSM2244461", "GSM2244462", "GSM2244463", "GSM2244464", "GSM2244465", "GSM2244466", "GSM2244467", "GSM2244468", "GSM2244469", "GSM2244470", "GSM2244471", "GSM2244472", "GSM2244473", "GSM2244474", "GSM2244475", "GSM2244476", "GSM2244477", "GSM2244478", "GSM2244479", "GSM2244480", "GSM2244481", "GSM2244482", "GSM2244483", "GSM2244484", "GSM2244485", "GSM2244486", "GSM2244487", "GSM2244488", "GSM2244489", "GSM2244490", "GSM2244491", "GSM2244492", "GSM2244493", "GSM2244494", "GSM2244495", "GSM2244496", "GSM2244497", "GSM2244498", "GSM2244499", "GSM2244500", "GSM2244501", "GSM2244502", "GSM2244503", "GSM2244504", "GSM2244505", "GSM2244506", "GSM2244507", "GSM2244508", "GSM2244509", "GSM2244510", "GSM2244511", "GSM2244512", "GSM2244513", "GSM2244514", "GSM2244515", "GSM2244516", "GSM2244517", "GSM2244518", "GSM2244519", "GSM2244520", "GSM2244521", "GSM2244522", "GSM2244523", "GSM2244524", "GSM2244525", "GSM2244526", "GSM2244527", "GSM2244528", "GSM2244529", "GSM2244530", "GSM2244531", "GSM2244532", "GSM2244533", "GSM2244534", "GSM2244535", "GSM2244536", "GSM2244537", "GSM2244538", "GSM2244539", "GSM2244540", "GSM2244541", "GSM2244542", "GSM2244543", "GSM2244544", "GSM2244545", "GSM2244546", "GSM2244547", "GSM2244548", "GSM2244549", "GSM2244550", "GSM2244551", "GSM2244552", "GSM2244553", "GSM2244554", "GSM2244555", "GSM2244556", "GSM2244557", "GSM2244558", "GSM2244559", "GSM2244560", "GSM2244561", "GSM2244562", "GSM2244563", "GSM2244564", "GSM2244565", "GSM2244566", "GSM2244567", "GSM2244568", "GSM2244569", "GSM2244570", "GSM2244571", "GSM2244572", "GSM2244573", "GSM2244574", "GSM2244575", "GSM2244576", "GSM2244577", "GSM2244578", "GSM2244579", "GSM2244580", "GSM2244581", "GSM2244582", "GSM2244583", "GSM2244584", "GSM2244585", "GSM2244586", "GSM2244587", "GSM2244588", "GSM2244589", "GSM2244590", "GSM2244591", "GSM2244592", "GSM2244593", "GSM2244594", "GSM2244595", "GSM2244596", "GSM2244597", "GSM2244598", "GSM2244599", "GSM2244600", "GSM2244601", "GSM2244602", "GSM2244603", "GSM2244604", "GSM2244605", "GSM2244606", "GSM2244607", "GSM2244608", "GSM2244609", "GSM2244610", "GSM2244611", "GSM2244612", "GSM2244613", "GSM2244614", "GSM2244615", "GSM2244616", "GSM2244617", "GSM2244618", "GSM2244619", "GSM2244620", "GSM2244621", "GSM2244622", "GSM2244623", "GSM2244624", "GSM2244625", "GSM2244626", "GSM2244627", "GSM2244628", "GSM2244629", "GSM2244630", "GSM2244631", "GSM2244632", "GSM2244633", "GSM2244634", "GSM2244635", "GSM2244636", "GSM2244637", "GSM2244638", "GSM2244639", "GSM2244640", "GSM2244641", "GSM2244642", "GSM2244643", "GSM2244644", "GSM2244645", "GSM2244646", "GSM2244647", "GSM2244648", "GSM2244649", "GSM2244650", "GSM2244651", "GSM2244652", "GSM2244653", "GSM2244654", "GSM2244655", "GSM2244656", "GSM2244657", "GSM2244658", "GSM2244659", "GSM2244660", "GSM2244661", "GSM2244662", "GSM2244663", "GSM2244664", "GSM2244665", "GSM2244666", "GSM2244667", "GSM2244668", "GSM2244669", "GSM2244670", "GSM2244671", "GSM2244672", "GSM2244673", "GSM2244674", "GSM2244675", "GSM2244676", "GSM2244677", "GSM2244678", "GSM2244679", "GSM2244680", "GSM2244681", "GSM2244682", "GSM2244683", "GSM2244684", "GSM2244685", "GSM2244686", "GSM2244687", "GSM2244688", "GSM2244689", "GSM2244690", "GSM2244691", "GSM2244692", "GSM2244693", "GSM2244694", "GSM2244695", "GSM2244696", "GSM2244697", "GSM2244698", "GSM2244699", "GSM2244700", "GSM2244701", "GSM2244702", "GSM2244703", "GSM2244704", "GSM2244705", "GSM2244706", "GSM2244707", "GSM2244708", "GSM2244709", "GSM2244710", "GSM2244711", "GSM2244712", "GSM2244713", "GSM2244714", "GSM2244715", "GSM2244716", "GSM2244717", "GSM2244718", "GSM2244719", "GSM2244720", "GSM2244721", "GSM2244722", "GSM2244723", "GSM2244724", "GSM2244725", "GSM2244726", "GSM2244727", "GSM2244728", "GSM2244729", "GSM2244730", "GSM2244731", "GSM2244732", "GSM2244733", "GSM2244734", "GSM2244735", "GSM2244736", "GSM2244737", "GSM2244738", "GSM2244739", "GSM2244740", "GSM2244741", "GSM2244742", "GSM2244743", "GSM2244744", "GSM2244745", "GSM2244746", "GSM2244747", "GSM2244748", "GSM2244749", "GSM2244750", "GSM2244751", "GSM2244752", "GSM2244753", "GSM2244754", "GSM2244755", "GSM2244756", "GSM2244757", "GSM2244758", "GSM2244759", "GSM2244760", "GSM2244761", "GSM2244762", "GSM2244763", "GSM2244764", "GSM2244765", "GSM2244766", "GSM2244767", "GSM2244768", "GSM2244769", "GSM2244770", "GSM2244771", "GSM2244772", "GSM2244773", "GSM2244774", "GSM2244775", "GSM2244776", "GSM2244777", "GSM2244778", "GSM2244779", "GSM2244780", "GSM2244781", "GSM2244782", "GSM2244783", "GSM2244784", "GSM2244785", "GSM2244786", "GSM2244787", "GSM2244788", "GSM2244789", "GSM2244790", "GSM2244791", "GSM2244792", "GSM2244793", "GSM2244794", "GSM2244795", "GSM2244796", "GSM2244797", "GSM2244798", "GSM2244799", "GSM2244800", "GSM2244801", "GSM2244802", "GSM2244803", "GSM2244804", "GSM2244805", "GSM2244806", "GSM2244807", "GSM2244808", "GSM2244809", "GSM2244810", "GSM2244811", "GSM2244812", "GSM2244813", "GSM2244814", "GSM2244815", "GSM2244816", "GSM2244817", "GSM2244818", "GSM2244819", "GSM2244820", "GSM2244821", "GSM2244822", "GSM2244823", "GSM2244824", "GSM2244825", "GSM2244826", "GSM2244827", "GSM2244828", "GSM2244829", "GSM2244830", "GSM2244831", "GSM2244832", "GSM2244833", "GSM2244834", "GSM2244835", "GSM2244836", "GSM2244837", "GSM2244838", "GSM2244839", "GSM2244840", "GSM2244841", "GSM2244842", "GSM2244843", "GSM2244844", "GSM2244845", "GSM2244846", "GSM2244847", "GSM2244848", "GSM2244849", "GSM2244850", "GSM2244851", "GSM2244852", "GSM2244853", "GSM2244854", "GSM2244855", "GSM2244856", "GSM2244857", "GSM2244858", "GSM2244859", "GSM2244860", "GSM2244861", "GSM2244862", "GSM2244863", "GSM2244864", "GSM2244865", "GSM2244866", "GSM2244867", "GSM2244868", "GSM2244869", "GSM2244870", "GSM2244871", "GSM2244872", "GSM2244873", "GSM2244874", "GSM2244875", "GSM2244876", "GSM2244877", "GSM2244878", "GSM2244879", "GSM2244880", "GSM2244881", "GSM2244882", "GSM2244883", "GSM2244884", "GSM2244885", "GSM2244886", "GSM2244887", "GSM2244888", "GSM2244889", "GSM2244890", "GSM2244891", "GSM2244892", "GSM2244893", "GSM2244894", "GSM2244895", "GSM2244896", "GSM2244897", "GSM2244898", "GSM2244899", "GSM2244900", "GSM2244901", "GSM2244902", "GSM2244903", "GSM2244904", "GSM2244905", "GSM2244906", "GSM2244907", "GSM2244908", "GSM2244909", "GSM2244910", "GSM2244911", "GSM2244912", "GSM2244913", "GSM2244914", "GSM2244915", "GSM2244916", "GSM2244917", "GSM2244918", "GSM2244919", "GSM2244920", "GSM2244921", "GSM2244922", "GSM2244923", "GSM2244924", "GSM2244925", "GSM2244926", "GSM2244927", "GSM2244928", "GSM2244929", "GSM2244930", "GSM2244931", "GSM2244932", "GSM2244933", "GSM2244934", "GSM2244935", "GSM2244936", "GSM2244937", "GSM2244938", "GSM2244939", "GSM2244940", "GSM2244941", "GSM2244942", "GSM2244943", "GSM2244944", "GSM2244945", "GSM2244946", "GSM2244947", "GSM2244948", "GSM2244949", "GSM2244950", "GSM2244951", "GSM2244952", "GSM2244953", "GSM2244954", "GSM2244955", "GSM2244956", "GSM2244957", "GSM2244958", "GSM2244959", "GSM2244960", "GSM2244961", "GSM2244962", "GSM2244963", "GSM2244964", "GSM2244965", "GSM2244966", "GSM2244967", "GSM2244968", "GSM2244969", "GSM2244970", "GSM2244971", "GSM2244972", "GSM2244973", "GSM2244974", "GSM2244975", "GSM2244976", "GSM2244977", "GSM2244978", "GSM2244979", "GSM2244980", "GSM2244981", "GSM2244982", "GSM2244983", "GSM2244984", "GSM2244985", "GSM2244986", "GSM2244987", "GSM2244988", "GSM2244989", "GSM2244990", "GSM2244991", "GSM2244992", "GSM2244993", "GSM2244994", "GSM2244995", "GSM2244996", "GSM2244997", "GSM2244998", "GSM2244999", "GSM2245000", "GSM2245001", "GSM2245002", "GSM2245003", "GSM2245004", "GSM2245005", "GSM2245006", "GSM2245007", "GSM2245008", "GSM2245009", "GSM2245010", "GSM2245011", "GSM2245012", "GSM2245013", "GSM2245014", "GSM2245015", "GSM2245016", "GSM2245017", "GSM2245018", "GSM2245019", "GSM2245020", "GSM2245021", "GSM2245022", "GSM2245023", "GSM2245024", "GSM2245025", "GSM2245026", "GSM2245027", "GSM2245028", "GSM2245029", "GSM2245030", "GSM2245031", "GSM2245032", "GSM2245033", "GSM2245034", "GSM2245035", "GSM2245036", "GSM2245037", "GSM2245038", "GSM2245039", "GSM2245040", "GSM2245041", "GSM2245042", "GSM2245043", "GSM2245044", "GSM2245045", "GSM2245046", "GSM2245047", "GSM2245048", "GSM2245049", "GSM2245050", "GSM2245051", "GSM2245052", "GSM2245053", "GSM2245054", "GSM2245055", "GSM2245056", "GSM2245057", "GSM2245058", "GSM2245059", "GSM2245060", "GSM2245061", "GSM2245062", "GSM2245063", "GSM2245064", "GSM2245065", "GSM2245066", "GSM2245067", "GSM2245068", "GSM2245069", "GSM2245070", "GSM2245071", "GSM2245072", "GSM2245073", "GSM2245074", "GSM2245075", "GSM2245076", "GSM2245077", "GSM2245078", "GSM2245079", "GSM2245080", "GSM2245081", "GSM2245082", "GSM2245083", "GSM2245084", "GSM2245085", "GSM2245086", "GSM2245087", "GSM2245088", "GSM2245089", "GSM2245090", "GSM2245091", "GSM2245092", "GSM2245093", "GSM2245094", "GSM2245095", "GSM2245096", "GSM2245097", "GSM2245098", "GSM2245099", "GSM2245100", "GSM2245101", "GSM2245102", "GSM2245103", "GSM2245104", "GSM2245105", "GSM2245106", "GSM2245107", "GSM2245108", "GSM2245109", "GSM2245110", "GSM2245111", "GSM2245112", "GSM2245113", "GSM2245114", "GSM2245115", "GSM2245116", "GSM2245117", "GSM2245118", "GSM2245119", "GSM2245120", "GSM2245121", "GSM2245122", "GSM2245123", "GSM2245124", "GSM2245125", "GSM2245126", "GSM2245127", "GSM2245128", "GSM2245129", "GSM2245130", "GSM2245131", "GSM2245132", "GSM2245133", "GSM2245134", "GSM2245135", "GSM2245136", "GSM2245137", "GSM2245138", "GSM2245139", "GSM2245140", "GSM2245141", "GSM2245142", "GSM2245143", "GSM2245144", "GSM2245145", "GSM2245146", "GSM2245147", "GSM2245148", "GSM2245149", "GSM2245150", "GSM2245151", "GSM2245152", "GSM2245153", "GSM2245154", "GSM2245155", "GSM2245156", "GSM2245157", "GSM2245158", "GSM2245159", "GSM2245160", "GSM2245161", "GSM2245162", "GSM2245163", "GSM2245164", "GSM2245165", "GSM2245166", "GSM2245167", "GSM2245168", "GSM2245169", "GSM2245170", "GSM2245171", "GSM2245172", "GSM2245173", "GSM2245174", "GSM2245175", "GSM2245176", "GSM2245177", "GSM2245178", "GSM2245179", "GSM2245180", "GSM2245181", "GSM2245182", "GSM2245183", "GSM2245184", "GSM2245185", "GSM2245186", "GSM2245187", "GSM2245188", "GSM2245189", "GSM2245190", "GSM2245191", "GSM2245192", "GSM2245193", "GSM2245194", "GSM2245195", "GSM2245196", "GSM2245197", "GSM2245198", "GSM2245199", "GSM2245200", "GSM2245201", "GSM2245202", "GSM2245203", "GSM2245204", "GSM2245205", "GSM2245206", "GSM2245207", "GSM2245208", "GSM2245209", "GSM2245210", "GSM2245211", "GSM2245212", "GSM2245213", "GSM2245214", "GSM2245215", "GSM2245216", "GSM2245217", "GSM2245218", "GSM2245219", "GSM2245220", "GSM2245221", "GSM2245222", "GSM2245223", "GSM2245224", "GSM2245225", "GSM2245226", "GSM2245227", "GSM2245228", "GSM2245229", "GSM2245230", "GSM2245231", "GSM2245232", "GSM2245233", "GSM2245234", "GSM2245235", "GSM2245236", "GSM2245237", "GSM2245238", "GSM2245239", "GSM2245240", "GSM2245241", "GSM2245242", "GSM2245243", "GSM2245244", "GSM2245245", "GSM2245246", "GSM2245247", "GSM2245248", "GSM2245249", "GSM2245250", "GSM2245251", "GSM2245252", "GSM2245253", "GSM2245254", "GSM2245255", "GSM2245256", "GSM2245257", "GSM2245258", "GSM2245259", "GSM2245260", "GSM2245261", "GSM2245262", "GSM2245263", "GSM2245264", "GSM2245265", "GSM2245266", "GSM2245267", "GSM2245268", "GSM2245269", "GSM2245270", "GSM2245271", "GSM2245272", "GSM2245273", "GSM2245274", "GSM2245275", "GSM2245276", "GSM2245277", "GSM2245278", "GSM2245279", "GSM2245280", "GSM2245281", "GSM2245282", "GSM2245283", "GSM2245284", "GSM2245285", "GSM2245286", "GSM2245287", "GSM2245288", "GSM2245289", "GSM2245290", "GSM2245291", "GSM2245292", "GSM2245293", "GSM2245294", "GSM2245295", "GSM2245296", "GSM2245297", "GSM2245298", "GSM2245299", "GSM2245300", "GSM2245301", "GSM2245302", "GSM2245303", "GSM2245304", "GSM2245305", "GSM2245306", "GSM2245307", "GSM2245308", "GSM2245309", "GSM2245310", "GSM2245311", "GSM2245312", "GSM2245313", "GSM2245314", "GSM2245315", "GSM2245316", "GSM2245317", "GSM2245318", "GSM2245319", "GSM2245320", "GSM2245321", "GSM2245322", "GSM2245323", "GSM2245324", "GSM2245325", "GSM2245326", "GSM2245327", "GSM2245328", "GSM2245329", "GSM2245330", "GSM2245331", "GSM2245332", "GSM2245333", "GSM2245334", "GSM2245335", "GSM2245336", "GSM2245337", "GSM2245338", "GSM2245339", "GSM2245340", "GSM2245341", "GSM2245342", "GSM2245343", "GSM2245344", "GSM2245345", "GSM2245346", "GSM2245347", "GSM2245348", "GSM2245349", "GSM2245350", "GSM2245351", "GSM2245352", "GSM2245353", "GSM2245354", "GSM2245355", "GSM2245356", "GSM2245357", "GSM2245358", "GSM2245359", "GSM2245360", "GSM2245361", "GSM2245362", "GSM2245363", "GSM2245364", "GSM2245365", "GSM2245366", "GSM2245367", "GSM2245368", "GSM2245369", "GSM2245370", "GSM2245371", "GSM2245372", "GSM2245373", "GSM2245374", "GSM2245375", "GSM2245376", "GSM2245377", "GSM2245378", "GSM2245379", "GSM2245380", "GSM2245381", "GSM2245382", "GSM2245383", "GSM2245384", "GSM2245385", "GSM2245386", "GSM2245387", "GSM2245388", "GSM2245389", "GSM2245390", "GSM2245391", "GSM2245392", "GSM2245393", "GSM2245394", "GSM2245395", "GSM2245396", "GSM2245397", "GSM2245398", "GSM2245399", "GSM2245400", "GSM2245401", "GSM2245402", "GSM2245403", "GSM2245404", "GSM2245405", "GSM2245406", "GSM2245407", "GSM2245408", "GSM2245409", "GSM2245410", "GSM2245411", "GSM2245412", "GSM2245413", "GSM2245414", "GSM2245415", "GSM2245416", "GSM2245417", "GSM2245418", "GSM2245419", "GSM2245420", "GSM2245421", "GSM2245422", "GSM2245423", "GSM2245424", "GSM2245425", "GSM2245426", "GSM2245427", "GSM2245428", "GSM2245429", "GSM2245430", "GSM2245431", "GSM2245432", "GSM2245433", "GSM2245434", "GSM2245435", "GSM2245436", "GSM2245437", "GSM2245438", "GSM2245439", "GSM2245440", "GSM2245441", "GSM2245442", "GSM2245443", "GSM2245444", "GSM2245445", "GSM2245446", "GSM2245447", "GSM2245448", "GSM2245449", "GSM2245450", "GSM2245451", "GSM2245452", "GSM2245453", "GSM2245454", "GSM2245455", "GSM2245456", "GSM2245457", "GSM2245458", "GSM2245459", "GSM2245460", "GSM2245461", "GSM2245462", "GSM2245463", "GSM2245464", "GSM2245465", "GSM2245466", "GSM2245467", "GSM2245468", "GSM2245469", "GSM2245470", "GSM2245471", "GSM2245472", "GSM2245473", "GSM2245474", "GSM2245475", "GSM2245476", "GSM2245477", "GSM2245478", "GSM2245479", "GSM2245480", "GSM2245481", "GSM2245482", "GSM2245483", "GSM2245484", "GSM2245485", "GSM2245486", "GSM2245487", "GSM2245488", "GSM2245489", "GSM2245490", "GSM2245491", "GSM2245492", "GSM2245493", "GSM2245494", "GSM2245495", "GSM2245496", "GSM2245497", "GSM2245498", "GSM2245499", "GSM2245500", "GSM2245501", "GSM2245502", "GSM2245503", "GSM2245504", "GSM2245505", "GSM2245506", "GSM2245507", "GSM2245508", "GSM2245509", "GSM2245510", "GSM2245511", "GSM2245512", "GSM2245513", "GSM2245514", "GSM2245515", "GSM2245516", "GSM2245517", "GSM2245518", "GSM2245519", "GSM2245520", "GSM2245521", "GSM2245522", "GSM2245523", "GSM2245524", "GSM2245525", "GSM2245526", "GSM2245527", "GSM2245528", "GSM2245529", "GSM2245530", "GSM2245531", "GSM2245532", "GSM2245533", "GSM2245534", "GSM2245535", "GSM2245536", "GSM2245537", "GSM2245538", "GSM2245539", "GSM2245540", "GSM2245541", "GSM2245542", "GSM2245543", "GSM2245544", "GSM2245545", "GSM2245546", "GSM2245547", "GSM2245548", "GSM2245549", "GSM2245550", "GSM2245551", "GSM2245552", "GSM2245553", "GSM2245554", "GSM2245555", "GSM2245556", "GSM2245557", "GSM2245558", "GSM2245559", "GSM2245560", "GSM2245561", "GSM2245562", "GSM2245563", "GSM2245564", "GSM2245565", "GSM2245566", "GSM2245567", "GSM2245568", "GSM2245569", "GSM2245570", "GSM2245571", "GSM2245572", "GSM2245573", "GSM2245574", "GSM2245575", "GSM2245576", "GSM2245577", "GSM2245578", "GSM2245579", "GSM2245580", "GSM2245581", "GSM2245582", "GSM2245583", "GSM2245584", "GSM2245585", "GSM2245586", "GSM2245587", "GSM2245588", "GSM2245589", "GSM2245590", "GSM2245591", "GSM2245592", "GSM2245593", "GSM2245594", "GSM2245595", "GSM2245596", "GSM2245597", "GSM2245598", "GSM2245599", "GSM2245600", "GSM2245601", "GSM2245602", "GSM2245603", "GSM2245604", "GSM2245605", "GSM2245606", "GSM2245607", "GSM2245608", "GSM2245609", "GSM2245610", "GSM2245611", "GSM2245612", "GSM2245613", "GSM2245614", "GSM2245615", "GSM2245616", "GSM2245617", "GSM2245618", "GSM2245619", "GSM2245620", "GSM2245621", "GSM2245622", "GSM2245623", "GSM2245624", "GSM2245625", "GSM2245626", "GSM2245627", "GSM2245628", "GSM2245629", "GSM2245630", "GSM2245631", "GSM2245632", "GSM2245633", "GSM2245634", "GSM2245635", "GSM2245636", "GSM2245637", "GSM2245638", "GSM2245639", "GSM2245640", "GSM2245641", "GSM2245642", "GSM2245643", "GSM2245644", "GSM2245645", "GSM2245646", "GSM2245647", "GSM2245648", "GSM2245649", "GSM2245650", "GSM2245651", "GSM2245652", "GSM2245653", "GSM2245654", "GSM2245655", "GSM2245656", "GSM2245657", "GSM2245658", "GSM2245659", "GSM2245660", "GSM2245661", "GSM2245662", "GSM2245663", "GSM2245664", "GSM2245665", "GSM2245666", "GSM2245667", "GSM2245668", "GSM2245669", "GSM2245670", "GSM2245671", "GSM2245672", "GSM2245673", "GSM2245674", "GSM2245675", "GSM2245676", "GSM2245677", "GSM2245678", "GSM2245679", "GSM2245680", "GSM2245681", "GSM2245682", "GSM2245683", "GSM2245684", "GSM2245685", "GSM2245686", "GSM2245687", "GSM2245688", "GSM2245689", "GSM2245690", "GSM2245691", "GSM2245692", "GSM2245693", "GSM2245694", "GSM2245695", "GSM2245696", "GSM2245697", "GSM2245698", "GSM2245699", "GSM2245700", "GSM2245701", "GSM2245702", "GSM2245703", "GSM2245704", "GSM2245705", "GSM2245706", "GSM2245707", "GSM2245708", "GSM2245709", "GSM2245710", "GSM2245711", "GSM2245712", "GSM2245713", "GSM2245714", "GSM2245715", "GSM2245716", "GSM2245717", "GSM2245718", "GSM2245719", "GSM2245720", "GSM2245721", "GSM2245722", "GSM2245723", "GSM2245724", "GSM2245725", "GSM2245726", "GSM2245727", "GSM2245728", "GSM2245729", "GSM2245730", "GSM2245731", "GSM2245732", "GSM2245733", "GSM2245734", "GSM2245735", "GSM2245736", "GSM2245737", "GSM2245738", "GSM2245739", "GSM2245740", "GSM2245741", "GSM2245742", "GSM2245743", "GSM2245744", "GSM2245745", "GSM2245746", "GSM2245747", "GSM2245748", "GSM2245749", "GSM2245750", "GSM2245751", "GSM2245752", "GSM2245753", "GSM2245754", "GSM2245755", "GSM2245756", "GSM2245757", "GSM2245758", "GSM2245759", "GSM2245760", "GSM2245761", "GSM2245762", "GSM2245763", "GSM2245764", "GSM2245765", "GSM2245766", "GSM2245767", "GSM2245768", "GSM2245769", "GSM2245770", "GSM2245771", "GSM2245772", "GSM2245773", "GSM2245774", "GSM2245775", "GSM2245776", "GSM2245777", "GSM2245778", "GSM2245779", "GSM2245780", "GSM2245781", "GSM2245782", "GSM2245783", "GSM2245784", "GSM2245785", "GSM2245786", "GSM2245787", "GSM2245788", "GSM2245789", "GSM2245790", "GSM2245791", "GSM2245792", "GSM2245793", "GSM2245794", "GSM2245795", "GSM2245796", "GSM2245797", "GSM2245798", "GSM2245799", "GSM2245800", "GSM2245801", "GSM2245802", "GSM2245803", "GSM2245804", "GSM2245805", "GSM2245806", "GSM2245807", "GSM2245808", "GSM2245809", "GSM2245810", "GSM2245811", "GSM2245812", "GSM2245813", "GSM2245814", "GSM2245815", "GSM2245816", "GSM2245817", "GSM2245818", "GSM2245819", "GSM2245820", "GSM2245821", "GSM2245822", "GSM2245823", "GSM2245824", "GSM2245825", "GSM2245826", "GSM2245827", "GSM2245828", "GSM2245829", "GSM2245830", "GSM2245831", "GSM2245832", "GSM2245833", "GSM2245834", "GSM2245835", "GSM2245836", "GSM2245837", "GSM2245838", "GSM2245839", "GSM2245840", "GSM2245841", "GSM2245842", "GSM2245843", "GSM2245844", "GSM2245845", "GSM2245846", "GSM2245847", "GSM2245848", "GSM2245849", "GSM2245850", "GSM2245851", "GSM2245852", "GSM2245853", "GSM2245854", "GSM2245855", "GSM2245856", "GSM2245857", "GSM2245858", "GSM2245859", "GSM2245860", "GSM2245861", "GSM2245862", "GSM2245863", "GSM2245864", "GSM2245865", "GSM2245866", "GSM2245867", "GSM2245868", "GSM2245869", "GSM2245870", "GSM2245871", "GSM2245872", "GSM2245873", "GSM2245874", "GSM2245875", "GSM2245876", "GSM2245877", "GSM2245878", "GSM2245879", "GSM2245880", "GSM2245881", "GSM2245882", "GSM2245883", "GSM2245884", "GSM2245885", "GSM2245886", "GSM2245887", "GSM2245888", "GSM2245889", "GSM2245890", "GSM2245891", "GSM2245892", "GSM2245893", "GSM2245894", "GSM2245895", "GSM2245896", "GSM2245897", "GSM2245898", "GSM2245899", "GSM2245900", "GSM2245901", "GSM2245902", "GSM2245903", "GSM2245904", "GSM2245905", "GSM2245906", "GSM2245907", "GSM2245908", "GSM2245909", "GSM2245910", "GSM2245911", "GSM2245912", "GSM2245913", "GSM2245914", "GSM2245915", "GSM2245916", "GSM2245917", "GSM2245918", "GSM2245919", "GSM2245920", "GSM2245921", "GSM2245922", "GSM2245923", "GSM2245924", "GSM2245925", "GSM2245926", "GSM2245927", "GSM2245928", "GSM2245929", "GSM2245930", "GSM2245931", "GSM2245932", "GSM2245933", "GSM2245934", "GSM2245935", "GSM2245936", "GSM2245937", "GSM2245938", "GSM2245939", "GSM2245940", "GSM2245941", "GSM2245942", "GSM2245943", "GSM2245945", "GSM2245948", "GSM2245950", "GSM2245952", "GSM2245955", "GSM2245957", "GSM2245959", "GSM2245961", "GSM2245965", "GSM2245966", "GSM2245968", "GSM2245971", "GSM2245972", "GSM2245974", "GSM2245976", "GSM2245977", "GSM2245980", "GSM2245981", "GSM2245982", "GSM2245983", "GSM2245984", "GSM2245985", "GSM2245986", "GSM2245987", "GSM2245988", "GSM2245989", "GSM2245990", "GSM2245991", "GSM2245992", "GSM2245993", "GSM2245994", "GSM2245995", "GSM2245996", "GSM2245997", "GSM2245998", "GSM2245999", "GSM2246000", "GSM2246001", "GSM2246002", "GSM2246003", "GSM2246004", "GSM2246005", "GSM2246006", "GSM2246007", "GSM2246008", "GSM2246009", "GSM2246010", "GSM2246011", "GSM2246012", "GSM2246013", "GSM2246014", "GSM2246015", "GSM2246016", "GSM2246017", "GSM2246018", "GSM2246019", "GSM2246020", "GSM2246021", "GSM2246022", "GSM2246023", "GSM2246024", "GSM2246025", "GSM2246026", 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"GSM2247045", "GSM2247046", "GSM2247047", "GSM2247048", "GSM2247049", "GSM2247050", "GSM2247051", "GSM2247052", "GSM2247053", "GSM2247054", "GSM2247055", "GSM2247056", "GSM2247057", "GSM2247058", "GSM2247059", "GSM2247060", "GSM2247061", "GSM2247062", "GSM2247063", "GSM2247064", "GSM2247065", "GSM2247066", "GSM2247067", "GSM2247068", "GSM2247069", "GSM2247070", "GSM2247071", "GSM2247072", "GSM2247073", "GSM2247074", "GSM2247075", "GSM2247076", "GSM2247077"], "sample_count": 3589, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Single-Cell RNAseq analysis of diffuse neoplastic infiltrating cells at the migrating front of human glioblastoma", "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:GSE138794 not downloaded", "asset:data:geo:GSE138794 licence not read", "asset:data:geo:GSE162631 not downloaded", "asset:data:geo:GSE162631 licence not read", "asset:data:geo:GSE84465 not downloaded", "asset:data:geo:GSE84465 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "KM"}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"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": 0.7, "band": "medium", "quote": "ROC analysis"}}, {"id": "method-5", "family": null, "specific": null, "label": "LASSO and multiCOX", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Based on 15 hub genes, a prognostic model was constructed using LASSO and multiCOX."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE162631", "GSE84465", "GSE138794"], "resolved_accessions": ["GSE162631", "GSE84465", "GSE138794"], "statements": ["The data could be obtained from TCGA database,or coresponding author after the requestion."], "basis": "The paper names GSE162631, GSE84465, GSE138794 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:39033204", "data:geo:GSE138794"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE138794"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:24:37Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11442, "completion_tokens": 1725, "cached_tokens": 264}}, "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:39033204", "type": "paper", "label": "pmid:39033204"}, {"id": "source:pmid:39033204", "type": "manuscript", "label": "PMID 39033204 full text"}, {"id": "data:geo:GSE138794", "type": "dataset", "label": "GEO GSE138794"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39033204", "type": "paper", "label": "pmid:39033204"}, {"id": "source:pmid:39033204", "type": "manuscript", "label": "PMID 39033204 full text"}, {"id": "data:geo:GSE138794", "type": "dataset", "label": "GEO GSE138794"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39033204", "type": "extraction", "used": ["source:pmid:39033204"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE138794", "type": "accession_resolution", "used": ["data:geo:GSE138794"], "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:39033204", "parent_hash": "sha256:e6cfa2e6cd417e96492cdd2bee03c1dd311e91bd7e2f0254e44fdbd828fc68fc", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE138794 licence not read", "asset:data:geo:GSE138794 not downloaded", "asset:data:geo:GSE162631 licence not read", "asset:data:geo:GSE162631 not downloaded", "asset:data:geo:GSE84465 licence not read", "asset:data:geo:GSE84465 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["o excessive blood vessel formation. METHODS: We enrolled bulk data of TCGA-LGG/GBM, CGGA-693, and CGG"], "order_basis": "paper_text_order:578", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["KM"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T02:49:06+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}}}