{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27903973", "kind": "science-record", "revision": 8, "content_hash": "sha256:f88b667a487bc5e48175682acab842bf638756ae045303519b374c10a83af255", "created_at": "2026-11-01T15:40:21Z", "updated_at": "2026-11-01T21:59:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Association of a cytarabine chemosensitivity related gene expression signature with survival in cytogenetically normal acute myeloid leukemia.", "doi": "10.18632/oncotarget.13650", "pmid": "27903973", "authors": ["Han Yan", "Lu Wen", "Dan Tan", "Pan Xie", "Feng-Mei Pang", "Hong-Hao Zhou", "Wei Zhang", "Zhao-Qian Liu", "Jie Tang", "Xi Li", "Xiao-Ping Chen"], "journal": "Oncotarget", "year": 2017, "abstract": "The prognosis of cytogenetically normal acute myeloid leukemia (CN-AML) varies greatly among patients. Achievement of complete remission (CR) after chemotherapy is indispensable for a better prognosis. To develop a gene signature predicting overall survival (OS) in CN-AML, we performed data mining procedure based on whole genome expression data of both blood cancer cell lines and AML patients from open access database. A gene expression signature including 42 probes was derived. These probes were significantly associated with both cytarabine half maximal inhibitory concentration values in blood cancer cell lines and OS in CN-AML patients. By using cox regression analysis and linear regression analysis, a chemo-sensitive score calculated algorithm based on mRNA expression levels of the 42 probes was established. The scores were associated with OS in both the training sample (p=5.13 × 10-4, HR=2.040, 95% CI: 1.364-3.051) and the validation sample (p=0.002, HR=2.528, 95% CI: 1.393-4.591) of the GSE12417 dataset from Gene Expression Omnibus. In The Cancer Genome Atlas (TCGA) CN-AML patients, higher scores were found to be associated with both worse OS (p=0.013, HR=2.442, 95% CI: 1.205-4.950) and DFS (p=0.015, HR=2.376, 95% CI: 1.181-4.779). Results of gene ontology (GO) analysis showed that all the significant GO Terms were correlated with cellular component of mitochondrion. In summary, a novel gene set that could predict prognosis of CN-AML was identified presently, which provided a new way to identify genes impacting AML chemo-sensitivity and prognosis.", "claims": [{"id": "claim-method", "statement": "Linear-regression analysis was performed to identify probes correlated with cytarabine IC50 in 96 blood cancer cell lines. Probes with P<0.05 were then selected for analysis in the GSE12417 dataset. Multivariate cox regression analysis (including age) was conducted to confirm whether the probes affect OS of CN-AML patients. Probes exhibited significance (p<0.05) in both the linear-regression analysis and the cox regression analysis in the same direction were screened.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27903973", "locator": "sections[14] \"Statistical analysis\" paragraph 2", "quote": "Linear-regression analysis was performed to identify probes correlated with cytarabine IC50 in 96 blood cancer cell lines. Probes with P<0.05 were then selected for analysis in the GSE12417 dataset. Multivariate cox regression analysis (including age) was conducted to confirm whether the probes affect OS of CN-AML patients. Probes exhibited significance (p<0.05) in both the linear-regression analysis and the cox regression analysis in the same direction were screened."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Based on GDSC release 5.0, 96 blood cancer cell lines with both natural log transformed IC50 values of cytarabine and normalized whole genome mRNA expression levels were selected in our study (Supplementary Table S1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27903973", "locator": "sections[11] \"GDSC cell lines\" paragraph 2", "quote": "Based on GDSC release 5.0, 96 blood cancer cell lines with both natural log transformed IC50 values of cytarabine and normalized whole genome mRNA expression levels were selected in our study (Supplementary Table S1)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using linear-regression and Cox regression analyses of cytarabine-response and AML survival data, the study derived a 42-probe chemo-sensitivity score that predicted poor outcomes in CN-AML and was validated in TCGA.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "The scores were associated with OS in both the training sample (p=5.13 × 10−4, HR=2.040, 95% CI: 1.364-3.051) and the validation sample (p=0.002, HR=2.528, 95% CI: 1.393-4.591) of the GSE12417 dataset from Gene Expression Omnibus."}, "evidence": [{"asset": "source:pmid:27903973", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "By using cox regression analysis and linear regression analysis, a chemo-sensitive score calculated algorithm based on mRNA expression levels of the 42 probes was established."}, {"asset": "source:pmid:27903973", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The scores were associated with OS in both the training sample (p=5.13 × 10−4, HR=2.040, 95% CI: 1.364-3.051) and the validation sample (p=0.002, HR=2.528, 95% CI: 1.393-4.591) of the GSE12417 dataset from Gene Expression Omnibus."}, {"asset": "source:pmid:27903973", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In The Cancer Genome Atlas (TCGA) CN-AML patients, higher scores were found to be associated with both worse OS (p=0.013, HR=2.442, 95% CI: 1.205-4.950) and DFS (p=0.015, HR=2.376, 95% CI: 1.181-4.779)."}, {"asset": "source:pmid:27903973", "locator": "sections[1] \"INTRODUCTION\" paragraph 5", "quote": "To find out whether genes correlated with chemo-sensitivity could also predict the outcome of AML, we downloaded IC50 values of cytarabine from 96 leukemia cell lines and raw whole genome expression data of these cell lines from GDSC in this study."}, {"asset": "source:pmid:27903973", "locator": "sections[1] \"INTRODUCTION\" paragraph 5", "quote": "Probes significantly associated with IC50 levels in the cells and OS in GSE12417 dataset, a whole genome expression dataset for CN-AML in NCBI Gene Expression Omnibus (GEO), were selected."}, {"asset": "source:pmid:27903973", "locator": "sections[1] \"INTRODUCTION\" paragraph 5", "quote": "Based on the selected probes, chemo-sensitivity score was derived and replicated in a TCGA CN-AML dataset."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using linear-regression and Cox regression analyses of cytarabine-response and AML survival data, the study derived a 42-probe chemo-sensitivity score that predicted poor outcomes in CN-AML and was validated in TCGA.", "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:27903973"], "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:GSE12417"], "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:GSE12417"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27903973", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.13650", "sha256": 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"resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:27903973:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6a139be4030befe6b5e9d123c06ae2faceff252088f136c735bca0784742aca8", "bytes": 3980, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T1", "version": null, "note": "Statistical analysis results for the 42 probes in blood cancer cell lines and in the GSE12417 dataset", "structure": {"pmcid": "PMC5352074", "section_index": 5, "section_title": "A 42 probe set correlated with both cytarabine sensitivity and AML OS", "row_count": 45, "column_count": 9}, "table": {"label": "Table 1", "caption": "Statistical analysis results for the 42 probes in blood cancer cell lines and in the GSE12417 dataset", "rows": [["Gene", "Probe name", "GDSC Blood cancer cell lines", "GSE12417", "Prognostic Index"], ["p value", "t value", "U133AB sample", "U133 Plus sample"], ["p value", "Z value", "p value", "Z value"], ["ULK1", "209333_at", "1.44E-05", "−4.578", "0.045", "−2.004", "0.018", "−2.362", "−0.309"], ["PIGF", "205078_at", "2.54E-05", "4.431", "0.043", "2.020", "0.041", "2.045", "0.193"], ["ABCC5", "209380_s_at", "9.26E-05", "−4.085", "0.011", "−2.541", "0.035", "−2.109", "−0.336"], ["MRPL40", "203152_at", "9.84E-05", "4.069", "0.003", "2.959", "0.018", "2.366", "0.253"], ["DARS2", "218365_s_at", "1.60E-04", "3.934", "0.046", "1.992", "0.011", "2.532", "0.193"], ["ITSN1", "35776_at", "2.27E-04", "−3.835", "0.027", "−2.208", "0.041", "−2.041", "−0.274"], ["ZC3HAV1", "213051_at", "4.09E-04", "−3.665", "0.032", "−2.149", "0.017", "−2.397", "−0.355"], ["NDUFB5", "203621_at", "5.32E-04", "3.588", "0.003", "3.022", "0.004", "2.865", "0.341"], ["SKAP2", "204361_s_at", "7.54E-04", "3.483", "0.025", "2.243", "0.038", "2.072", "0.186"], ["ZNF451", "215012_at", "0.001", "−3.367", "0.038", "−2.070", "0.005", "−2.821", "−0.316"], ["IARS2", "217900_at", "0.002", "3.197", "0.010", "2.562", "0.018", "2.358", "0.212"], ["MPP1", "202974_at", "0.003", "−3.049", "0.018", "−2.367", "0.044", "−2.010", "−0.363"], ["ZNF259P1/ZPR1", "217185_s_at", "0.004", "2.961", "0.003", "3.023", "0.011", "2.541", "0.231"], ["BCL2L1", "212312_at", "0.004", "−2.916", "0.022", "−2.288", "0.042", "−2.032", "−0.309"], ["CHMP4A/TM9SF1", "218572_at", "0.006", "2.836", "0.026", "2.219", "0.047", "1.987", "0.197"], ["GAS2", "205848_at", "0.007", "2.744", "0.029", "2.185", "0.001", "3.403", "0.191"], ["ME2", "210154_at", "0.008", "2.715", "0.021", "2.307", "0.016", "2.412", "0.221"], ["ALCAM", "201951_at", "0.008", "2.710", "0.000", "3.634", "0.000", "5.064", "0.363"], ["DNAJC1", "218409_s_at", "0.009", "2.675", "0.005", "2.791", "0.023", "2.282", "0.259"], ["VDAC1", "212038_s_at", "0.009", "2.673", "0.005", "2.804", "0.018", "2.376", "0.213"], ["SLC25A38", "217961_at", "0.009", "−2.648", "0.011", "−2.540", "0.016", "−2.420", "−0.314"], ["IL6R", "205945_at", "0.010", "2.636", "0.003", "2.986", "0.022", "2.282", "0.260"], ["ME2", "210153_s_at", "0.012", "2.568", "0.018", "2.367", "0.002", "3.053", "0.254"], ["ETFDH", "33494_at", "0.013", "2.527", "0.040", "2.058", "0.043", "2.020", "0.158"], ["TAL1", "206283_s_at", "0.017", "−2.441", "0.036", "−2.092", "0.027", "−2.216", "−0.339"], ["TAL1", "216925_s_at", "0.017", "−2.427", "0.011", "−2.541", "0.032", "−2.147", "−0.381"], ["BMP2K", "219546_at", "0.017", "−2.420", "0.013", "−2.486", "0.033", "−2.137", "−0.308"], ["FH", "203033_x_at", "0.019", "2.379", "0.016", "2.399", "0.033", "2.131", "0.213"], ["SLC14A1", "205856_at", "0.021", "−2.353", "0.037", "−2.091", "0.048", "−1.974", "−0.356"], ["SPATS2", "218324_s_at", "0.021", "2.338", "0.023", "2.268", "0.017", "2.391", "0.272"], ["P4HTM", "222125_s_at", "0.026", "2.269", "0.013", "2.478", "0.029", "2.184", "0.212"], ["PLA2G4A", "210145_at", "0.031", "2.195", "0.007", "2.689", "0.023", "2.281", "0.242"], ["TRIB2", "202478_at", "0.031", "−2.184", "0.030", "−2.174", "0.033", "−2.126", "−0.310"], ["ACYP2/LOC101927144", "206833_s_at", "0.032", "2.182", "0.008", "2.636", "0.030", "2.167", "0.321"], ["SYNCRIP", "217834_s_at", "0.033", "2.166", "0.025", "2.239", "0.007", "2.691", "0.211"], ["IDH3A", "202069_s_at", "0.033", "2.161", "0.012", "2.509", "0.014", "2.466", "0.215"], ["TPD52", "201688_s_at", "0.033", "2.161", "0.004", "2.895", "0.008", "2.662", "0.268"], ["HIST1H2APS4", "216585_at", "0.033", "2.160", "0.038", "2.072", "0.005", "2.795", "0.229"], ["ERMP1", "218342_s_at", "0.036", "2.124", "0.034", "2.119", "0.038", "2.072", "0.217"], ["SLC25A37", "221920_s_at", "0.038", "−2.099", "0.016", "−2.413", "0.027", "−2.213", "−0.368"], ["TCTN3", "212121_at", "0.046", "2.026", "0.000", "3.506", "0.009", "2.620", "0.331"], ["CD164", "208654_s_at", "0.048", "2.008", "0.012", "2.519", "0.006", "2.732", "0.293"]], "row_count": 45, "column_count": 9, "numeric_cells": 348, "header_rows": 3, "locator": "section[5]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:27903973:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8f0e39e42ec617fe6fad4941d2e396a420f1f8e0ba587fa2e76fc094c87a4c17", "bytes": 595, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#T2", "version": null, "note": "Four most significantly GO terms for the selected 42 probes", "structure": {"pmcid": "PMC5352074", "section_index": 5, "section_title": "A 42 probe set correlated with both cytarabine sensitivity and AML OS", "row_count": 5, "column_count": 6}, "table": {"label": "Table 2", "caption": "Four most significantly GO terms for the selected 42 probes", "rows": [["Category", "GO Term", "Count", "%", "p value", "Bonferroni"], ["GOTERM_CC_FAT", "GO:0044429 ~ mitochondrial part", "12", "30.0", "1.54E-07", "1.74E-05"], ["GOTERM_CC_FAT", "GO:0005759 ~ mitochondrial matrix", "7", "17.5", "2.18E-05", "0.002"], ["GOTERM_CC_FAT", "GO:0031980 ~ mitochondrial lumen", "7", "17.5", "2.18E-05", "0.002"], ["GOTERM_CC_FAT", "GO:0005739 ~ mitochondrion", "12", "30.0", "5.36E-05", "0.006"]], "row_count": 5, "column_count": 6, "numeric_cells": 20, "header_rows": 1, "locator": "section[5]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:27903973:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5166dff6e682258e67b60e093f4a0f7fd345bc68b9bfe0f71f28a822bbe2b3f2", "bytes": 778, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#T3", "version": null, "note": "Comparison of chemo-sensitivity score between genotypes of well-known somatic mutations affecting AML outcome", "structure": {"pmcid": "PMC5352074", "section_index": 7, "section_title": "Validation of the association between 42-probe-based chemo-sensitivity score and survival in TCGA CN-AML patients", "row_count": 9, "column_count": 6}, "table": {"label": "Table 3", "caption": "Comparison of chemo-sensitivity score between genotypes of well-known somatic mutations affecting AML outcome", "rows": [["Mutation", "Wild type", "Mutation", "p value"], ["Score (Mean±SD)", "N", "Score (Mean±SD)", "N", ""], ["CEBPA", "0.612±3.561", "48", "−2.557±3.428", "5", "0.063"], ["DNMT3A R882", "−0.109±3.396", "42", "1.926±4.239", "11", "0.099"], ["FLT3-IDT", "−0.185±3.705", "36", "1.369±3.355", "17", "0.148"], ["IDH", "0.780±3.849", "39", "−0.986±2.683", "14", "0.120"], ["NPM1", "−0.022±3.925", "21", "0.533±3.485", "32", "0.592"], ["RUNX1", "0.295±3.740", "49", "0.535±2.373", "4", "0.901"], ["WT1", "0.354±3.762", "48", "−0.076±2.379", "5", "0.804"]], "row_count": 9, "column_count": 6, "numeric_cells": 36, "header_rows": 2, "locator": "section[7]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:GSE12417 not downloaded", "asset:data:geo:GSE12417 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Linear-regression analysis was performed to identify probes correlated with cytarabine IC50 in 96 blood cancer cell lines. Probes with P<0.05 were then selected for analysis in the GSE12417 dataset. Multivariate cox regression analysis (including age) was conducted to confirm whether the probes affect OS of CN-AML patients. Probes exhibited significance (p<0.05) in both the linear-regression analysis and the cox regression analysis in the same direction were screened."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.7, "band": "medium", "quote": "linear regression"}}, {"id": "method-4", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "blast"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "alignment_identity", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": []}, "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": ["GSE12417"], "resolved_accessions": ["GSE12417"], "statements": ["Based on GDSC release 5.0, 96 blood cancer cell lines with both natural log transformed IC50 values of cytarabine and normalized whole genome mRNA expression levels were selected in our study (Supplementary Table S1)."], "basis": "The paper names GSE12417 in NCBI 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:27903973", "data:geo:GSE12417", "asset:table:pmid:27903973:1", "asset:table:pmid:27903973:2", "asset:table:pmid:27903973:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12417"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:30:07Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 81630, "completion_tokens": 6737, "cached_tokens": 2104}}, "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:27903973", "type": "paper", "label": "pmid:27903973"}, {"id": "source:pmid:27903973", "type": "manuscript", "label": "PMID 27903973 full text"}, {"id": "data:geo:GSE12417", "type": "dataset", "label": "GEO GSE12417"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27903973", "type": "paper", "label": "pmid:27903973"}, {"id": "source:pmid:27903973", "type": "manuscript", "label": "PMID 27903973 full text"}, {"id": "data:geo:GSE12417", "type": "dataset", "label": "GEO GSE12417"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27903973", "type": "extraction", "used": ["source:pmid:27903973"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12417", "type": "accession_resolution", "used": ["data:geo:GSE12417"], "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:27903973", "parent_hash": "sha256:aa251089c12357aa70f2c24555a2104274edeac81a0a73447097d602cacb8eca", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE12417 licence not read", "asset:data:geo:GSE12417 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ect the whole genome mRNA expression levels: Affymetrix GeneChip Human Genome U133A and U133B arrays", "rrays (U133 AB sample) for 163 patients, and Affymetrix GeneChip Human Genome U133 plus 2.0 array (U", "ession level of this dataset was detected by Affymetrix GeneChip Human Genome U133 plus 2.0 array an"], "order_basis": "paper_text_order:4467", "id": "assay:1"}, {"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": ["Linear-regression analysis was performed to identify probes correlated with cytarabine IC50 in 96 blood cancer cell lines. Probes with P<0.05 were then selected for analysis in the GSE12417 dataset. Multivariate cox regression analysis (including age) was conducted to confirm whether the probes affect OS of CN-AML patients. Probes exhibited significance (p<0.05) in both the linear-regression analysis and the cox regression analysis in the same direction were screened."], "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":"2026-11-04T00:42:26+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}}}