{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27246976", "kind": "science-record", "revision": 9, "content_hash": "sha256:65a860a2576013ff27d2b26714dce76e8fe16bbe911a99e317c0a1f6b025f1c9", "created_at": "2026-11-01T15:40:18Z", "updated_at": "2026-11-01T22:42:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Long noncoding RNA ZFAS1 promotes gastric cancer cells proliferation by epigenetically repressing KLF2 and NKD2 expression.", "doi": "10.18632/oncotarget.9611", "pmid": "27246976", "authors": ["Fengqi Nie", "Xiang Yu", "Mingde Huang", "Yunfei Wang", "Min Xie", "Hongwei Ma", "Zhaoxia Wang", "Wei De", "Ming Sun"], "journal": "Oncotarget", "year": 2017, "abstract": "Recently, long noncoding RNAs have been emerged as critical regulators of human disease and prognostic markers in several cancers, including gastric cancer. In this study, we globally assessed the transcriptomic differences of lncRNAs in gastric cancer using publicly available microarray data from Gene Expression Omnibus (GEO) and identified an oncogenetic lncRNA ZFAS1, which may promote gastric tumorigenesis. ZFAS1 has been found to be upregulated and function as oncogene in colorectal cancer and hepatocellular carcinoma, but its expression pattern, biological function and underlying mechanism in gastric cancer is still undetermined. Here, we reported that ZFAS1 expression is also overexpressed in gastric cancer, and its increased level is associated with poor prognosis and shorter survival. Knockdown of ZFAS1 impaired gastric cancer cells proliferation and induced apoptosis in vitro, and inhibited tumorigenicity of gastric cancer cells in vivo. Mechanistically, RNA immunoprecipitation and RNA pull-down experiment showed that ZFAS1 could simultaneously interact with EZH2 and LSD1/CoREST to repress underlying targets KLF2 and NKD2 transcription. In addition, rescue experiments determined that ZFAS1 oncogenic function is partly dependent on repressing KLF2 and NKD2. Taken together, our findings illuminate how ZFAS1 over-expression confers an oncogenic function in gastric cancer.", "claims": [{"id": "claim-method", "statement": "The Students t test (2 tailed), one-way ANOVA, and Mann-Whitney U test were conducted to analyze the in vitro and in vivo data by SPSS 17.0 software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27246976", "locator": "sections[25] \"Statistical analysis\" paragraph 2", "quote": "The Students t test (2 tailed), one-way ANOVA, and Mann-Whitney U test were conducted to analyze the in vitro and in vivo data by SPSS 17.0 software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27246976", "locator": "sections[13] \"Microarray data analysis\" paragraph 2", "quote": "Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper’s headline result is that ZFAS1 is overexpressed in gastric cancer and its increased level is associated with poor prognosis and shorter survival: “Here, we reported that ZFAS1 expression is also overexpressed in gastric cancer, and its increased level is associated with poor prognosis and shorter survival.” No numerical result is stated for the registered target, which is a statistical method and data route rather than a numerical outcome.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27246976", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we reported that ZFAS1 expression is also overexpressed in gastric cancer, and its increased level is associated with poor prognosis and shorter survival."}, {"asset": "source:pmid:27246976", "locator": "sections[25] \"Statistical analysis\" paragraph 2", "quote": "The Students t test (2 tailed), one-way ANOVA, and Mann-Whitney U test were conducted to analyze the in vitro and in vivo data by SPSS 17.0 software. P values less than 0.05 were considered significant."}, {"asset": "source:pmid:27246976", "locator": "sections[13] \"Microarray data analysis\" paragraph 2", "quote": "Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA)."}, {"asset": "source:pmid:27246976", "locator": "sections[3] \"lncRNA ZFAS1 is overexpressed in gastric cancer tissues and cell lines\" paragraph 2", "quote": "To identify lncRNAs involved in gastric cancer development and progression, four microarray datasets (GSE37023, GSE13911,GSE65801 and GSE51575) were obtained from GEO to analyze lncRNAs alterations between gastric cancer and pair nontumor tissues."}, {"asset": "source:pmid:27246976", "locator": "sections[3] \"lncRNA ZFAS1 is overexpressed in gastric cancer tissues and cell lines\" paragraph 2", "quote": "In addition, analysis of TCGA stomach and normal tissues RNA sequencing data also showed that ZFAS1 expression is up-regulated in tumor tissues compared with normal tissues (Figure 1C)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper’s headline result is that ZFAS1 is overexpressed in gastric cancer and its increased level is associated with poor prognosis and shorter survival: “Here, we reported that ZFAS1 expression is also overexpressed in gastric cancer, and its increased level is associated with poor prognosis and shorter survival.” No numerical result is stated for the registered target, which is a statistical method and data route rather than a numerical outcome.", "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:27246976"], "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:GSE13911"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE13911"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27246976", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.9611", "sha256": "sha256:6c65bf98c39c49d16bc93e0ede21d888f06baa8869a733db661dbad9f1a2bc54", "bytes": 31801, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/oncotarget.9611", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5503528", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13911", "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=GSE13911", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13911", "version": null, "note": "Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM350411", "GSM350412", "GSM350413", "GSM350414", "GSM350415", "GSM350416", "GSM350417", "GSM350418", "GSM350419", "GSM350420", "GSM350421", "GSM350422", "GSM350423", "GSM350424", "GSM350425", "GSM350426", "GSM350427", "GSM350428", "GSM350429", "GSM350430", "GSM350431", "GSM350432", "GSM350433", "GSM350434", "GSM350435", "GSM350436", "GSM350437", "GSM350438", "GSM350439", "GSM350440", "GSM350441", "GSM350442", "GSM350443", "GSM350444", "GSM350445", "GSM350446", "GSM350447", "GSM350448", "GSM350449", "GSM350450", "GSM350451", "GSM350452", "GSM350453", "GSM350454", "GSM350455", "GSM350456", "GSM350457", "GSM350458", "GSM350459", "GSM350460", "GSM350461", "GSM350462", "GSM350463", "GSM350464", "GSM350465", "GSM350466", "GSM350467", "GSM350468", "GSM350469", "GSM350470", "GSM350471", "GSM350472", "GSM350473", "GSM350474", "GSM350475", "GSM350476", "GSM350477", "GSM350478", "GSM350479"], "sample_count": 69, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from primary gastric tumors (MSI and MSS) and adjacent normal samples", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE37023", "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=GSE37023", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37023", "version": null, "note": "Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM908687", "GSM908688", "GSM908689", "GSM908690", "GSM908691", "GSM908692", "GSM908693", "GSM908694", "GSM908695", "GSM908696", "GSM908697", "GSM908698", "GSM908699", "GSM908700", "GSM908701", "GSM908702", "GSM908703", "GSM908704", "GSM908705", "GSM908706", "GSM908707", "GSM908708", "GSM908709", "GSM908710", "GSM908711", "GSM908712", "GSM908713", "GSM908714", "GSM908715", "GSM908716", "GSM908717", "GSM908718", "GSM908719", "GSM908720", "GSM908721", "GSM908722", "GSM908723", "GSM908724", "GSM908725", "GSM908726", "GSM908727", "GSM908728", "GSM908729", "GSM908730", "GSM908731", "GSM908732", "GSM908733", "GSM908734", "GSM908735", "GSM908736", "GSM908737", "GSM908738", "GSM908739", "GSM908740", "GSM908741", "GSM908742", "GSM908743", "GSM908744", "GSM908745", "GSM908746", "GSM908747", "GSM908748", "GSM908749", "GSM908750", "GSM908751", "GSM908752", "GSM908753", "GSM908754", "GSM908755", "GSM908756", "GSM908757", "GSM908758", "GSM908759", "GSM908760", "GSM908761", "GSM908762", "GSM908763", "GSM908764", "GSM908765", "GSM908766", "GSM908767", "GSM908768", "GSM908769", "GSM908770", "GSM908771", "GSM908772", "GSM908773", "GSM908774", "GSM908775", "GSM908776", "GSM908777", "GSM908778", "GSM908779", "GSM908780", "GSM908781", "GSM908782", "GSM908783", "GSM908784", "GSM908785", "GSM908786", "GSM908787", "GSM908788", "GSM908789", "GSM908790", "GSM908791", "GSM908792", "GSM908793", "GSM908794", "GSM908795", "GSM908796", "GSM908797", "GSM908798", "GSM908799", "GSM908800", "GSM908801", "GSM908802", "GSM908803", "GSM908804", "GSM908805", "GSM908806", "GSM908807", "GSM908808", "GSM908809", "GSM908810", "GSM908811", "GSM908812", "GSM908813", "GSM908814", "GSM908815", "GSM908816", "GSM908817", "GSM908818", "GSM908819", "GSM908820", "GSM908821", "GSM908822", "GSM908823", "GSM908824", "GSM908825", "GSM908826", "GSM908827", "GSM908828", "GSM908829", "GSM908830", "GSM908831", "GSM908832", "GSM908833", "GSM908834", "GSM908835", "GSM908836", "GSM908837", "GSM908838", "GSM908839", "GSM908840", "GSM908841", "GSM908842", "GSM908843", "GSM908844", "GSM908845", "GSM908846", "GSM908847", "GSM908848", "GSM908849", "GSM908850", "GSM908851", "GSM908852", "GSM908853", "GSM908854", "GSM908855", "GSM908856", "GSM908857", "GSM908858", "GSM908859", "GSM908860", "GSM908861", "GSM908862", "GSM908863", "GSM908864", "GSM908865", "GSM908866", "GSM908867", "GSM908868", "GSM908869", "GSM908870", "GSM908871", "GSM908872", "GSM908873", "GSM908874", "GSM908875", "GSM908876", "GSM908877", "GSM908878", "GSM908879", "GSM908880", "GSM908881", "GSM908882", "GSM908883", "GSM908884", "GSM908885", "GSM908886", "GSM908887", "GSM908888", "GSM908889", "GSM908890", "GSM908891", "GSM908892", "GSM908893", "GSM908894", "GSM908895", "GSM908896", "GSM908897", "GSM908898", "GSM908899", "GSM908900", "GSM908901", "GSM908902", "GSM908903", "GSM908904", "GSM908905", "GSM908906", "GSM908907", "GSM908908", "GSM908909", "GSM908910", "GSM908911", "GSM908912", "GSM908913", "GSM908914", "GSM908915", "GSM908916", "GSM908917", "GSM908918", "GSM908919", "GSM908920", "GSM908921", "GSM908922", "GSM908923", "GSM908924", "GSM908925", "GSM908926", "GSM908927", "GSM908928", "GSM908929", "GSM908930", "GSM908931", "GSM908932", "GSM908933", "GSM908934", "GSM908935", "GSM908936"], "sample_count": 250, "group_sizes": null, "group_sizes_basis": null, "platform": "96;97;2834", "taxon": "Homo sapiens", "title": "Comprehensive Genomic Meta-analysis Identifies Intra-Tumoral Stroma as a Predictor of Gastric Cancer Patient Survival", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE51575", "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=GSE51575", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE51575", "version": null, "note": "Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1248612", "GSM1248613", "GSM1248614", "GSM1248615", "GSM1248616", "GSM1248617", "GSM1248618", "GSM1248619", "GSM1248620", "GSM1248621", "GSM1248622", "GSM1248623", "GSM1248624", "GSM1248625", "GSM1248626", "GSM1248627", "GSM1248628", "GSM1248629", "GSM1248630", "GSM1248631", "GSM1248632", "GSM1248633", "GSM1248634", "GSM1248635", "GSM1248636", "GSM1248637", "GSM1248638", "GSM1248639", "GSM1248640", "GSM1248641", "GSM1248642", "GSM1248643", "GSM1248644", "GSM1248645", "GSM1248646", "GSM1248647", "GSM1248648", "GSM1248649", "GSM1248650", "GSM1248651", "GSM1248652", "GSM1248653", "GSM1248654", "GSM1248655", "GSM1248656", "GSM1248657", "GSM1248660", "GSM1248661", "GSM1248662", "GSM1248663", "GSM1248664", "GSM1248665"], "sample_count": 52, "group_sizes": null, "group_sizes_basis": null, "platform": "13607", "taxon": "Homo sapiens", "title": "mRNA Expression Profiling in EBV-postive Gastric Carcinoma and EBV-negative GC in comparison with their normal mucosa tissue", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE65801", "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=GSE65801", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65801", "version": null, "note": "Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1606492", "GSM1606493", "GSM1606494", "GSM1606495", "GSM1606496", "GSM1606497", "GSM1606498", "GSM1606499", "GSM1606500", "GSM1606501", "GSM1606502", "GSM1606503", "GSM1606504", "GSM1606505", "GSM1606506", "GSM1606507", "GSM1606508", "GSM1606509", "GSM1606510", "GSM1606511", "GSM1606512", "GSM1606513", "GSM1606514", "GSM1606515", "GSM1606516", "GSM1606517", "GSM1606518", "GSM1606519", "GSM1606520", "GSM1606521", "GSM1606522", "GSM1606523", "GSM1606524", "GSM1606525", "GSM1606526", "GSM1606527", "GSM1606528", "GSM1606529", "GSM1606530", "GSM1606531", "GSM1606532", "GSM1606533", "GSM1606534", "GSM1606535", "GSM1606536", "GSM1606537", "GSM1606538", "GSM1606539", "GSM1606540", "GSM1606541", "GSM1606542", "GSM1606543", "GSM1606544", "GSM1606545", "GSM1606546", "GSM1606547", "GSM1606548", "GSM1606549", "GSM1606550", "GSM1606551", "GSM1606552", "GSM1606553", "GSM1606554", "GSM1606555"], "sample_count": 64, "group_sizes": null, "group_sizes_basis": null, "platform": "14550", "taxon": "Homo sapiens", "title": "Characterization of differentially expressed genes involved in pathways associated with gastric cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:27246976:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6e5a1935d170d33e914280201c05d52b971fa1cc01c8399873013571102a9587", "bytes": 893, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T1", "version": null, "note": "Correlation between ZFAS1 expression and clinicopathological characteristics of gastric cancer patients (n=54)", "structure": {"pmcid": "PMC5503528", "section_index": 4, "section_title": "ZFAS1 amplification is correlated with poor prognosis in gastric cancer", "row_count": 21, "column_count": 5}, "table": {"label": "Table 1", "caption": "Correlation between ZFAS1 expression and clinicopathological characteristics of gastric cancer patients (n=54)", "rows": [["Characteristics", "", "ZFAS1", "P value"], ["Low", "High"], ["Age", "<50", "12", "13", "0.500"], ["", ">50", "15", "14", ""], ["Gender", "Male", "11", "15", "0.207"], ["", "Fmale", "16", "12", ""], ["location", "Distal", "12", "7", "0.314"], ["", "Middle", "10", "15", ""], ["", "Proximal", "5", "5", ""], ["Tumor size", "<5cm", "17", "8", "0.014*"], ["", ">5cm", "10", "19", ""], ["Histologic", "Well", "1", "2", "0.05*"], ["", "Moderately", "12", "4", ""], ["", "Poorly", "9", "18", ""], ["", "Undifferentiated", "5", "3", ""], ["Lymphatic metastasis", "NO", "11", "15", "0.207"], ["", "YES", "16", "12", ""], ["TNM stages", "I", "6", "0", "0.001*"], ["", "II", "13", "5", ""], ["", "III", "8", "20", ""], ["", "IV", "0", "2", ""]], "row_count": 21, "column_count": 5, "numeric_cells": 49, "header_rows": 2, "locator": "section[4]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:GSE13911 not downloaded", "asset:data:geo:GSE13911 licence not read", "asset:data:geo:GSE37023 not downloaded", "asset:data:geo:GSE37023 licence not read", "asset:data:geo:GSE51575 not downloaded", "asset:data:geo:GSE51575 licence not read", "asset:data:geo:GSE65801 not downloaded", "asset:data:geo:GSE65801 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Students t test (2 tailed), one-way ANOVA, and Mann-Whitney U test were conducted to analyze the in vitro and in vivo data by SPSS 17.0 software."}}, {"id": "method-2", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann-Whitney"}}, {"id": "method-3", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_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": "R1", "reachable": true, "accessions": ["GSE37023", "GSE13911", "GSE65801", "GSE51575"], "resolved_accessions": ["GSE37023", "GSE13911", "GSE65801", "GSE51575"], "statements": ["Four human microarray datasets including GSE37023, GSE13911, GSE65801 and GSE51575 were obtained from public GEO database (http://www.ncbi.nlm.nih.gov/geo) and normalized using Robust Multichip Average (RMA)."], "basis": "The paper names GSE37023, GSE13911, GSE65801, GSE51575 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:27246976", "data:geo:GSE13911", "asset:table:pmid:27246976:1"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13911"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:34Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 66359, "completion_tokens": 4745, "cached_tokens": 2096}}, "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:27246976", "type": "paper", "label": "pmid:27246976"}, {"id": "source:pmid:27246976", "type": "manuscript", "label": "PMID 27246976 full text"}, {"id": "data:geo:GSE13911", "type": "dataset", "label": "GEO GSE13911"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27246976", "type": "paper", "label": "pmid:27246976"}, {"id": "source:pmid:27246976", "type": "manuscript", "label": "PMID 27246976 full text"}, {"id": "data:geo:GSE13911", "type": "dataset", "label": "GEO GSE13911"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27246976", "type": "extraction", "used": ["source:pmid:27246976"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13911", "type": "accession_resolution", "used": ["data:geo:GSE13911"], "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:27246976", "parent_hash": "sha256:027e1623396463d0a0c2e79cbb65e05b14f09d95bda9ae3e42e0512f53b799c1", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE13911 licence not read", "asset:data:geo:GSE13911 not downloaded", "asset:data:geo:GSE37023 licence not read", "asset:data:geo:GSE37023 not downloaded", "asset:data:geo:GSE51575 licence not read", "asset:data:geo:GSE51575 not downloaded", "asset:data:geo:GSE65801 licence not read", "asset:data:geo:GSE65801 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["ed with poor prognosis and shorter survival. Knockdown of ZFAS1 impaired gastric cancer cells proli"], "order_basis": "paper_text_order:883", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["stric cancer cells proliferation and induced apoptosis in vitro, and inhibited tumorigenicity of ga"], "order_basis": "paper_text_order:958", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["bited tumorigenicity of gastric cancer cells in vivo. Mechanistically, RNA immunoprecipitation an", "t were conducted to analyze the in vitro and in vivo data by SPSS 17.0 software. P values less th"], "order_basis": "paper_text_order:1031", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Students t test (2 tailed), one-way ANOVA, and Mann-Whitney U test were conducted to analyze the in vitro and in vivo data by SPSS 17.0 software."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]},"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":"2026-11-04T01:59:12+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}}}