← All .science files
pmid:25944691
Activation of insulin-like growth factor 1 receptor in patients with non-small cell lung cancer.
Jin-Soo Kim · Edward S Kim · Diane Liu · J Jack Lee · Carmen Behrens · Scott M Lippman · Waun Ki Hong · Ignacio I Wistuba · Euni Lee · Ho-Young Lee
Oncotarget · 2015 doi:10.18632/oncotarget.3796
Paper
complete
Experiment
partial
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 10 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[2] object · 6 fields
evidence array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
data object · 3 fields
assets array · 5 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 34 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 items
[9] array · 2 items
[10] array · 2 items
[11] array · 2 items
[12] array · 2 items
[13] array · 2 items
[14] array · 2 items
[15] array · 2 items
[16] array · 2 items
[17] array · 2 items
[18] array · 2 items
[19] array · 2 items
[20] array · 2 items
[21] array · 2 items
[22] array · 2 items
[23] array · 2 items
[24] array · 2 items
[25] array · 2 items
[26] array · 2 items
[27] array · 2 items
[28] array · 2 items
[29] array · 2 items
[30] array · 2 items
[31] array · 2 items
[32] array · 2 items
[33] array · 2 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 41 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 items
[9] array · 2 items
[10] array · 2 items
[11] array · 2 items
[12] array · 2 items
[13] array · 2 items
[14] array · 2 items
[15] array · 2 items
[16] array · 2 items
[17] array · 2 items
[18] array · 2 items
[19] array · 2 items
[20] array · 2 items
[21] array · 2 items
[22] array · 2 items
[23] array · 2 items
[24] array · 2 items
[25] array · 2 items
[26] array · 2 items
[27] array · 2 items
[28] array · 2 items
[29] array · 2 items
[30] array · 2 items
[31] array · 2 items
[32] array · 2 items
[33] array · 2 items
[34] array · 2 items
[35] array · 2 items
[36] array · 2 items
[37] array · 2 items
[38] array · 2 items
[39] array · 2 items
[40] array · 2 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 15 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 17 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
gaps array · 0 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 0 items
resolved_accessions array · 0 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 5 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[1] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25944691", "kind": "science-record", "revision": 7, "content_hash": "sha256:3a525b5836b5d4dba998c9166375a58bbcbfb45bf386829c28203ef4fa938616", "created_at": "2026-11-01T15:40:08Z", "updated_at": "2026-11-01T21:58:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Activation of insulin-like growth factor 1 receptor in patients with non-small cell lung cancer.", "doi": "10.18632/oncotarget.3796", "pmid": "25944691", "authors": ["Jin-Soo Kim", "Edward S Kim", "Diane Liu", "J Jack Lee", "Carmen Behrens", "Scott M Lippman", "Waun Ki Hong", "Ignacio I Wistuba", "Euni Lee", "Ho-Young Lee"], "journal": "Oncotarget", "year": 2015, "abstract": "According to previous reports demonstrating the implication of insulin-like growth factor receptor (IGF-1R) signaling in non-small cell lung cancer (NSCLC), in this study, the potential prognostic values of IGF-1R expression/activation were analyzed. The expression and activation of IGF-1R were evaluated in two tissue microarray (TMA) sets from NSCLC patients (N = 352 for TMA I, and N = 353 for TMA II). Alterations in IGF-1R protein or mRNA expression in NSCLC patients were evaluated using publicly available data from The Cancer Genome Atlas (TCGA). We found that membranous and cytoplasmic IGF-1R expressions were significantly associated with squamous cell carcinoma (SCC) in both of the TMAs. Analysis of the TCGA data revealed increased mRNA levels in NSCLC patients, which was significantly associated with reductions in overall survival (OS) (median survival 26.51 vs. 47.77 months, P = 0.017) and disease-free survival (median survival 17.44 vs. 37.65 months, P = 0.045) only in NSCLC patients with adenocarcinoma (ADC). These data suggest that IGF-1R is activated in patients with NSCLC, particularly those with SCC. IGF-1R mRNA expression is a potential prognostic factor in patients with NSCLC, especially those with ADC. Further studies are warranted to investigate the prognostic value of IGF-1R in NSCLC patients.", "claims": [{"id": "claim-method", "statement": "The association between changes in IGF-1R mRNA expression and OS or DFS was evaluated by a log-rank test and provided by the TCGA Research Network [27, 28].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25944691", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "The association between changes in IGF-1R mRNA expression and OS or DFS was evaluated by a log-rank test and provided by the TCGA Research Network [27, 28]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We obtained archived formalin-fixed and paraffin-embedded samples from previously described tissue banks at The University of Texas M.D. Anderson Cancer Center (Houston, TX) [23]. The tissue specimens were originally collected between 1997 and 2005 and were classified using the 2004 World Health Organization classification system [25].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25944691", "locator": "sections[9] \"Case selection and TMA construction\" paragraph 2", "quote": "We obtained archived formalin-fixed and paraffin-embedded samples from previously described tissue banks at The University of Texas M.D. Anderson Cancer Center (Houston, TX) [23]. The tissue specimens were originally collected between 1997 and 2005 and were classified using the 2004 World Health Organization classification system [25]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In TCGA NSCLC data, increased IGF-1R mRNA expression was associated with shorter overall and disease-free survival in patients with adenocarcinoma.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25944691", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Analysis of the TCGA data revealed increased mRNA levels in NSCLC patients, which was significantly associated with reductions in overall survival (OS) (median survival 26.51 vs. 47.77 months, P = 0.017) and disease-free survival (median survival 17.44 vs. 37.65 months, P = 0.045) only in NSCLC patients with adenocarcinoma (ADC)."}, {"asset": "source:pmid:25944691", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "The association between changes in IGF-1R mRNA expression and OS or DFS was evaluated by a log-rank test and provided by the TCGA Research Network [27, 28]."}, {"asset": "source:pmid:25944691", "locator": "sections[11] \"IGF-1R mRNA and protein expression and survival from The Cancer Genome Atlas (TCGA) data\" paragraph 2", "quote": "The TCGA Research Network portal was used for evaluating alterations in mRNA and protein expression, and clinical data for comparing survival; these are available at www.cbioportal.org/public-portal [27, 28]."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "In TCGA NSCLC data, increased IGF-1R mRNA expression was associated with shorter overall and disease-free survival in patients with adenocarcinoma.", "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:25944691"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25944691", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.3796", "sha256": "sha256:fbb57f174f56f7999902392bd7554848415f54f742246501bd21c328decbce03", "bytes": 20114, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/oncotarget.3796", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4599304", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:25944691:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3060b50f2f8eb4e5a726083e5c724bc5c7a3933e43591c779886650af63cc910", "bytes": 1007, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T1", "version": null, "note": "Patients characteristics in tissue microarray (TMA) dataset I", "structure": {"pmcid": "PMC4599304", "section_index": 3, "section_title": "Expression of IGF-1R and pIGF-1R", "row_count": 34, "column_count": 2}, "table": {"label": "Table 1", "caption": "Patients characteristics in tissue microarray (TMA) dataset I", "rows": [["Characteristic", "TMA I (N=352)"], ["Median age", ""], ["Years (Range)", "66 (34-90)"], ["Gender", ""], ["Female", "189 (53.7%)"], ["Male", "160 (45.5%)"], ["Histology", ""], ["Adenocarcinoma", "231 (65.6%)"], ["Squamous cell carcinoma", "121 (34.3%)"], ["Ethnicity", ""], ["Caucasian", "313 (88.9%)"], ["Asian", "14 (4.0%)"], ["African American", "15 (4.3%)"], ["Hispanic", "10 (2.8%)"], ["Smoking status*", ""], ["Never", "63 (17.9%)"], ["Former", "174 (49.4%)"], ["Current", "114 (32.4%)"], ["Unknown", "1 (0.3%)"], ["Pathological T stage†", ""], ["T1", "130 (36.9%)"], ["T2", "185 (52.6%)"], ["T3", "18 (5.1%)"], ["T4", "20 (5.7%)"], ["Pathological N stage†", ""], ["N0", "253 (71.9%)"], ["N1", "60 (17.0%)"], ["N2", "39 (11.1%)"], ["Nx", ""], ["Final Stage†", ""], ["I", "225 (63.9%)"], ["II", "65 (18.5%)"], ["III", "50 (14.2%)"], ["IV", "12 (3.4%)"]], "row_count": 34, "column_count": 2, "numeric_cells": 25, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:25944691:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:144a9dfcef2cadf9470bfc3c9ae15f800c18fd5947866da2f1b6b9f29c48db4b", "bytes": 1176, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#T2", "version": null, "note": "Patients characteristics in tissue microarray (TMA) dataset II", "structure": {"pmcid": "PMC4599304", "section_index": 3, "section_title": "Expression of IGF-1R and pIGF-1R", "row_count": 41, "column_count": 2}, "table": {"label": "Table 2", "caption": "Patients characteristics in tissue microarray (TMA) dataset II", "rows": [["Characteristic", "TMA II (N=353)"], ["Median age", ""], ["Years (Range)", "66 (34-90)"], ["Gender", ""], ["Female", "174 (49.3%)"], ["Male", "179 (50.7%)"], ["Histology", ""], ["Adenocarcinoma", "227 (64.3%)"], ["Squamous cell carcinoma", "126 (35.7%)"], ["Ethnicity", ""], ["Caucasian", "316 (89.5%)"], ["Asian", "5(1.4%)"], ["African American", "18 (5.1%)"], ["Hispanic", "14 (4%)"], ["Smoking status*", ""], ["Never", "38 (10.8%)"], ["Former", "164 (46.5%)"], ["Current", "151 (42.8%)"], ["Unknown", ""], ["Pathological T stage†", ""], ["T1", "131(37.1%)"], ["T2", "202(57.2%)"], ["T3", "20(5.7%)"], ["Pathological N stage†", ""], ["N0", "236 (67.6%)"], ["N1", "66 (18.9%)"], ["N2", "47 (13.5%)"], ["Final Stage†", ""], ["IA", "100 (28.3%)"], ["IB", "125 (35.4%)"], ["IIA", "22 (6.2%)"], ["IIB", "49 (13.9%)"], ["IIIA", "57(16.1%)"], ["Adjuvant treatment", ""], ["No", "216 (61.2%)"], ["Yes", "119 (33.7%)"], ["Unknown", "18 (5.1%)"], ["Neoadjuvant treatment", ""], ["No", "298 (84.4%)"], ["Yes", "52 (14.7%)"], ["Unknown", "3 (0.8%)"]], "row_count": 41, "column_count": 2, "numeric_cells": 30, "header_rows": 1, "locator": "section[3]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:25944691:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4cd7fe4cf8369c77d19d58b109546654ab884a155410fd556f4902734c1235b6", "bytes": 1184, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T3", "version": null, "note": "Univariate analyses of clinical prognostic factors and biomarkers (TMA I)", "structure": {"pmcid": "PMC4599304", "section_index": 4, "section_title": "Recurrence-free survival and overall survival", "row_count": 15, "column_count": 5}, "table": {"label": "Table 3", "caption": "Univariate analyses of clinical prognostic factors and biomarkers (TMA I)", "rows": [["Variable", "HR for OS (95% CI)", "p-value", "HR for RFS (95% CI)", "p-value*"], ["Age", ".997 (.979-1.015)", ".723", "1.040 (1.025-1.056)", "<.0001"], ["Gender (M vs.F)", ".813 (.549-1.203)", ".300", "1.324 (.981-1.786)", ".066"], ["Race (white vs. other)", "2.123 (1.261-3.574)", ".005", "1.043 (.640-1.699)", ".867"], ["Smoker (Ever vs. never)", ".669 (418-1.072)", ".095", "1.136 (.754-1.712)", ".542"], ["Histology (ADC vs. SCC)", ".946 (.626-1.430)", ".792", "1.442 (1.068-1.949)", ".017"], ["Stage (vs. I)", "", "", "", ""], ["II", "2.005 (1.201-3346)", ".008", "1.566 (1.069-2.293)", ".021"], ["III/IV", "4.106 (2.557-6.593)", "<.001", "2.707 (1.365-5.370)", ".004"], ["IGF-1R", "", "", "", ""], ["cytoplasmic", ".998 (.993-1.003)", ".381", "1.000 (.997-1.003)", ".961"], ["membrane", ".995 (.988-1.003)", ".238", "1.000 (.995-1.005)", ".962"], ["p-IGF-IR/1R", "", "", "", ""], ["cytoplasmic", "1.008 (.987-1.030)", ".444", "1.011 (.996-1.026)", ".141"], ["membrane", "1.004 (.999-1.009)", ".157", "1.004 (.999-1.008)", ".099"]], "row_count": 15, "column_count": 5, "numeric_cells": 48, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:25944691:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:54f335ffb77a4b2623f3e5ff5d4945af406889623ab11142163ae5a4803fdf48", "bytes": 1312, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[2]#T4", "version": null, "note": "Univariate analyses of clinical prognostic factors and biomarkers (TMA II)", "structure": {"pmcid": "PMC4599304", "section_index": 4, "section_title": "Recurrence-free survival and overall survival", "row_count": 17, "column_count": 5}, "table": {"label": "Table 4", "caption": "Univariate analyses of clinical prognostic factors and biomarkers (TMA II)", "rows": [["Variable", "HR for OS (95% CI)", "p-value", "HR for RFS (95% CI)", "p-value*"], ["Age", "1.015 (0.998-1.031)", "0.08", "1.007 (0.993-1.022)", "0.31"], ["Gender (M vs.F)", "1.468 (1.067-2.020)", "0.0186", "1.317 (0.997-1.740)", "0.053"], ["Race (white vs. other)", "0.747 (0.457-1.222)", "0.245", "0.784 (0.504-1.222)", "0.28"], ["Smoker", "", "", "", ""], ["Former vs. Never", "1.045 (0.597-1.828)", "0.88", "1.081 (0.667-1.751)", "0.75"], ["Current vs. Never", "1.219 (0.698-2.129)", "0.49", "1.108 (0.681-1.803)", "0.68"], ["Histology (ADC vs. SCC)", "0.831 (0.600-1.151)", "0.27", "0.809 (0.609-1.074)", "0.14"], ["Stage (vs. I)", "", "", "", ""], ["II", "1.608 (1.090-2.374)", "0.0157", "1.73 (1.226-2.440)", "0.0018"], ["IIIA", "2.399 (1.613-3.570)", "<0.0001", "2.734 (1.930-3.872)", "<0.0001"], ["IGF-IR", "", "", "", ""], ["cytoplasmic", "1.003 (0.999-1.007)", "0.19", "1.004 (1.000-1.008)", "0.034"], ["membrane", "1.002 (0.992-1.011)", "0.70", "1.001 (0.992-1.010)", "0.88"], ["p-IGF-112/IR", "", "", "", ""], ["cytoplasmic", "0.997 (0.985-1.010)", "0.50", "0.990 (0.978-1.003)", "0.12"], ["membrane", "0.998 (0.993-1.003)", "0.41", "0.997 0.992-1.001", "0.16"]], "row_count": 17, "column_count": 5, "numeric_cells": 51, "header_rows": 1, "locator": "section[4]/table-wrap[2]#T4"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The association between changes in IGF-1R mRNA expression and OS or DFS was evaluated by a log-rank test and provided by the TCGA Research Network [27, 28]."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["We obtained archived formalin-fixed and paraffin-embedded samples from previously described tissue banks at The University of Texas M.D. Anderson Cancer Center (Houston, TX) [23]. The tissue specimens were originally collected between 1997 and 2005 and were classified using the 2004 World Health Organization classification system [25]."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:25944691", "asset:table:pmid:25944691:1", "asset:table:pmid:25944691:2", "asset:table:pmid:25944691:3", "asset:table:pmid:25944691:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:23:53Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 41205, "completion_tokens": 4839, "cached_tokens": 10784}}, "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:25944691", "type": "paper", "label": "pmid:25944691"}, {"id": "source:pmid:25944691", "type": "manuscript", "label": "PMID 25944691 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25944691", "type": "paper", "label": "pmid:25944691"}, {"id": "source:pmid:25944691", "type": "manuscript", "label": "PMID 25944691 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25944691", "type": "extraction", "used": ["source:pmid:25944691"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:25944691", "parent_hash": "sha256:f4366c58dacbb9528c55eac732e6904d66f27572cbf4446dada8b7c54ed5fe61", "fork_of": null, "generation": 6}, "gaps": ["execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": ["ation of IGF-1R were evaluated in two tissue microarray (TMA) sets from NSCLC patients (N = 352 for", "baseline characteristics from the two tissue microarray (TMA) sets are presented in Tables 1 and 2."], "order_basis": "paper_text_order:372", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The association between changes in IGF-1R mRNA expression and OS or DFS was evaluated by a log-rank test and provided by the TCGA Research Network [27, 28]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}