{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29088836", "kind": "science-record", "revision": 6, "content_hash": "sha256:ce527a47d7a3b9367f3e279d18e21bd0159e8f057698e383a8a65305dfc1b1b5", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T21:21:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Common, germline genetic variations in the novel tumor suppressor BAP1 and risk of developing different types of cancer.", "doi": "10.18632/oncotarget.20465", "pmid": "29088836", "authors": ["Moubin Lin", "Liren Zhang", "Michelle A T Hildebrandt", "Maosheng Huang", "Xifeng Wu", "Yuanqing Ye"], "journal": "Oncotarget", "year": 2017, "abstract": "BRCA1 associated protein-1 (BAP1) is a novel tumor suppressor that has recently been shown to be somatically mutated in several cancers. The BAP1 gene also carries rare germline mutations in families with a high incidence of several types of cancers, such as mesothelioma, uveal melanoma, lung adenocarcinoma, melanocytic neoplasms, and renal cell carcinoma. To test the hypothesis that common, germline genetic variants in BAP1 may also contribute to the risk of developing different types of cancer, we genotyped germline single nucleotide polymorphisms (SNPs) for BAP1 in a large population of patients with cancer, including 2,340 with colorectal cancer, 1,436 with bladder cancer, 3,313 with lung cancer, 1,325 with renal cell carcinoma, and 1,162 with esophageal cancer. We identified significant association of rs11708581 (P = 0.0034) and rs390802 (P = 0.015) with risk of renal cell carcinoma and rs12163565 (P = 0.038) with risk of lung cancer. Expression quantitative trait loci analysis in renal cell carcinoma using publicly available data from TCGA showed that the proxy SNPs for rs11708581 and rs390802 were negatively associated with the expression level of BAP1. Our study indicate that common germline genetic variants of BAP1 play a role in mediating the risk of developing renal cell carcinoma and lung cancer.", "claims": [{"id": "claim-method", "statement": "The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29088836", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data on renal clear cell carcinoma were downloaded from The Cancer Genome Atlas (TCGA, dbGaP Study Accession: phs000178.v9.p8, data portal: https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp). Expression data (RNA-seq) and methylation (HumanMethylation450 chip) were measured in tumor samples, somatic copy number was inferred from the tumor samples and paired normal controls (Affymetrix SNP 6.0 platform), and genotyping data were measured from blood derived DNA samples (Affymetrix SNP 6.0 platform).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29088836", "locator": "sections[13] \"Expression quantitative trait loci (eQTL) analysis\" paragraph 2", "quote": "Data on renal clear cell carcinoma were downloaded from The Cancer Genome Atlas (TCGA, dbGaP Study Accession: phs000178.v9.p8, data portal: https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp). Expression data (RNA-seq) and methylation (HumanMethylation450 chip) were measured in tumor samples, somatic copy number was inferred from the tumor samples and paired normal controls (Affymetrix SNP 6.0 platform), and genotyping data were measured from blood derived DNA samples (Affymetrix SNP 6.0 platform)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study found that common germline BAP1 variants were associated with renal cell carcinoma and lung cancer risk; cancer-risk associations were analyzed by unconditional multivariate logistic regression, while potential BAP1-expression mechanisms were assessed through eQTL analysis of TCGA renal clear cell carcinoma data.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types."}, "evidence": [{"asset": "source:pmid:29088836", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our study indicate that common germline genetic variants of BAP1 play a role in mediating the risk of developing renal cell carcinoma and lung cancer."}, {"asset": "source:pmid:29088836", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types."}, {"asset": "source:pmid:29088836", "locator": "sections[13] \"Expression quantitative trait loci (eQTL) analysis\" paragraph 2", "quote": "Data on renal clear cell carcinoma were downloaded from The Cancer Genome Atlas (TCGA, dbGaP Study Accession: phs000178.v9.p8, data portal: https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study found that common germline BAP1 variants were associated with renal cell carcinoma and lung cancer risk; cancer-risk associations were analyzed by unconditional multivariate logistic regression, while potential BAP1-expression mechanisms were assessed through eQTL analysis of TCGA renal clear cell carcinoma data.", "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:29088836"], "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:29088836", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.20465", "sha256": "sha256:9255f4e3a0317f1ed5234db6437f9aa93e96d2cfe533d76d2296e49e85a1dba8", "bytes": 37793, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/oncotarget.20465", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5650391", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:29088836:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:45cb84534fa16c8454d7bb367e5699b9f6d7a9b376f14d7e6b4a1458931cc896", "bytes": 1698, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T1", "version": null, "note": "Study populations", "structure": {"pmcid": "PMC5650391", "section_index": 3, "section_title": "Host characteristics", "row_count": 46, "column_count": 4}, "table": {"label": "Table 1", "caption": "Study populations", "rows": [["Variables", "Cases, N(%)", "Controls, N(%)", "P-value"], ["Bladder Cancer", ""], ["Total", "1436", "1436", ""], ["Age, mean(SD)", "65.40(11.09)", "65.40(11.07)", "1.00"], ["Sex", "", "", "1.00"], ["Male", "1147(80)", "1147(80)", ""], ["Female", "289(20)", "289(20)", ""], ["Smoking status", "", "", "<0.001"], ["Never", "340(28)", "491(34)", ""], ["Ever", "877(72)", "941(66)", ""], ["Colorectal Cancer", ""], ["Total", "2340", "2340", ""], ["Age, mean(SD)", "56.48(11.89)", "56.52(11.83)", "0.91"], ["Sex", "", "", "1.00"], ["Male", "1350(58)", "1350(58)", ""], ["Female", "990(42)", "990(42)", ""], ["Smoking status", "", "", "<0.001"], ["Never", "1270(54)", "899(39)", ""], ["Ever", "1070(46)", "1432(61)", ""], ["Esophageal Cancer", ""], ["Total", "1162", "1162", ""], ["Age, mean(SD)", "62.67(10.76)", "62.68(10.74)", "0.99"], ["Sex", "", "", "1.00"], ["Male", "1027(88)", "1027(88)", ""], ["Female", "135(12)", "135(12)", ""], ["Smoking status", "", "", "<0.001"], ["Never", "270(27)", "398(34)", ""], ["Ever", "718(73)", "760(66)", ""], ["Renal Cell Carcinoma", ""], ["Total", "1325", "1325", ""], ["Age, mean(SD)", "59.54(10.80)", "59.54(10.78)", "1.00"], ["Sex", "", "", "1.00"], ["Male", "882(66.57)", "882(67)", ""], ["Female", "443(33.43)", "443(33)", ""], ["Smoking status", "", "", "<0.001"], ["Never", "580(46)", "488(37)", ""], ["Ever", "687(54)", "834(63)", ""], ["Lung Cancer", ""], ["Total", "3313", "3313", ""], ["Age, mean(SD)", "62.40(10.81)", "62.32(10.78)", "0.78"], ["Sex", "", "", "1.00"], ["Male", "1824(55)", "1824(55)", ""], ["Female", "1489(45)", "1489(45)", ""], ["Smoking status", "", "", "1.00"], ["Never", "589(18)", "589(18)", ""], ["Ever", "2724(82)", "2724(82)", ""]], "row_count": 46, "column_count": 4, "numeric_cells": 75, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:29088836:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dfbc1b4f20f108c9bdc3a55d14a9d700206568b74ceb97600eac37d7626ae9ed", "bytes": 2394, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T2", "version": null, "note": "Effects of BAP1 genetic variation on the risk of developing different types of cancer", "structure": {"pmcid": "PMC5650391", "section_index": 4, "section_title": "BAP1 genetic variants and risk of developing different types of cancer", "row_count": 31, "column_count": 6}, "table": {"label": "Table 2", "caption": "Effects of BAP1 genetic variation on the risk of developing different types of cancer", "rows": [["SNP", "Cases, N (cc/cv/vv)", "Control, N (cc/cv/vv)", "Model", "*OR(95% CI)", "p-value"], ["Bladder Cancer"], ["rs11708581", "1066\\310\\16", "1064\\325\\23", "Dom", "0.90(0.74-1.10)", "0.30"], ["rs123598", "1260\\135\\1", "1272\\133\\2", "Dom", "1.04(0.79-1.36)", "0.79"], ["rs12163565", "893\\461\\50", "945\\422\\53", "Dom", "1.17(0.99-1.39)", "0.070"], ["rs390802", "922\\427\\40", "941\\422\\46", "Dom", "0.99(0.83-1.18)", "0.89"], ["rs13094687", "617\\632\\135", "613\\631\\163", "Dom", "1.06(0.89-1.26)", "0.51"], ["Esophageal Cancer", "", "", "", ""], ["rs11708581", "880\\247\\20", "848\\261\\20", "Dom", "0.94(0.76-1.16)", "0.54"], ["rs123598", "1033\\114\\2", "1046\\95\\2", "Dom", "1.07(0.79-1.45)", "0.67"], ["rs12163565", "755\\340\\33", "759\\345\\39", "Dom", "1.00(0.83-1.21)", "1.00"], ["rs390802", "772\\333\\37", "758\\344\\33", "Dom", "0.93(0.77-1.13)", "0.49"], ["rs13094687", "502\\488\\135", "516\\484\\142", "Dom", "1.00(0.88-1.13)", "0.96"], ["Renal Cell Carcinoma", "", "", "", ""], ["rs11708581", "1028\\251\\9", "982\\295\\18", "Dom", "0.74(0.61-0.91)", "0.0034"], ["rs123598", "1173\\127\\1", "1169\\123\\3", "Dom", "0.99(0.71-1.38)", "0.95"], ["rs12163565", "825\\420\\56", "861\\391\\55", "Dom", "1.05(0.86-1.29)", "0.62"], ["rs390802", "918\\340\\34", "861\\400\\35", "Dom", "0.80(0.67-0.96)", "0.015"], ["rs13094687", "571\\584\\139", "613\\547\\136", "Dom", "1.09(0.93-1.28)", "0.30"], ["Lung Cancer", "", "", "", "", ""], ["rs11708581", "2521\\685\\41", "2467\\721\\42", "Dom", "0.93(0.82-1.04)", "0.21"], ["rs123598", "2937\\320\\3", "2900\\330\\6", "Dom", "0.93(0.79-1.10)", "0.39"], ["rs12163565", "2060\\1073\\135", "2122\\1001\\129", "Dom", "1.11(1.01-1.24)", "0.038"], ["rs390802", "2207\\970\\76", "2163\\970\\94", "Dom", "0.96(0.86-1.06)", "0.41"], ["rs13094687", "1476\\1435\\342", "1468\\1404\\357", "Dom", "1.00(0.90-1.11)", "0.99"], ["Colorectal Cancer", "", "", "", ""], ["rs11708581", "1767\\503\\30", "1744\\514\\29", "Dom", "1.00(0.86-1.17)", "0.80"], ["rs123598", "2083\\224\\1", "2056\\234\\2", "Dom", "0.89(0.72-1.09)", "0.93"], ["rs12163565", "1506\\729\\89", "1501\\700\\95", "Dom", "1.07(0.94-1.22)", "0.30"], ["rs390802", "1553\\690\\61", "1526\\697\\64", "Dom", "0.97(0.85-1.11)", "0.73"], ["rs13094687", "1062\\1024\\230", "1054\\992\\241", "Dom", "1.00(0.88-1.13)", "0.96"]], "row_count": 31, "column_count": 6, "numeric_cells": 126, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:29088836:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:51101f06ccf990dd007f4d8c92baa9f586312c1e8cc6573d3711a69adf6d79c2", "bytes": 1995, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T3", "version": null, "note": "Effect of BAP1 genetic variants by sex, smoking status, and age", "structure": {"pmcid": "PMC5650391", "section_index": 5, "section_title": "Stratified analysis for BAP1 genetic variants and risk of of developing different types of cancer", "row_count": 28, "column_count": 7}, "table": {"label": "Table 3", "caption": "Effect of BAP1 genetic variants by sex, smoking status, and age", "rows": [["SNP", "Group", "Case N(cc/cv/vv)", "Control N (cc/cv/vv)", "Model", "*OR(95% CI)", "P-value"], ["Sex"], ["Renal Cell Carcinoma", "", "", "", "", ""], ["rs11708581", "Male", "689\\165\\5", "652\\197\\16", "Dom", "0.75(0.60-0.95)", "0.017"], ["", "Female", "339\\86\\4", "330\\98\\2", "Dom", "0.88(0.63-1.23)", "0.45"], ["rs390802", "Male", "625\\217\\22", "575\\263\\26", "Dom", "0.77(0.63-0.95)", "0.014"], ["", "Female", "293\\123\\12", "286\\137\\9", "Dom", "0.93(0.69-1.25)", "0.65"], ["Lung", "", "", "", "", "", ""], ["rs12163565", "Male", "1128\\594\\73", "1203\\531\\59", "Dom", "1.19(1.04-1.37)", "0.013"], ["", "Female", "932\\479\\62", "919\\470\\70", "Dom", "0.99(0.85-1.15)", "0.90"], ["Smoking Status"], ["Renal Cell Carcinoma", "", "", "", "", ""], ["rs11708581", "Never", "447\\109\\6", "372\\103\\6", "Dom", "0.87(0.65-1.17)", "0.36"], ["", "Ever", "538\\128\\3", "607\\192\\12", "Dom", "0.73(0.57-0.94)", "0.014"], ["rs390802", "Never", "390\\159\\14", "329\\140\\11", "Dom", "0.96(0.74-1.25)", "0.78"], ["", "Ever", "485\\168\\18", "529\\260\\24", "Dom", "0.73(0.58-0.91)", "0.0051"], ["Lung", "", "", "", "", "", ""], ["rs12163565", "Never", "377\\187\\18", "375\\177\\29", "Dom", "1.00(0.78-1.27)", "0.98"], ["", "Ever", "1683\\886\\117", "1747\\824\\100", "Dom", "1.12(1.00-1.26)", "0.047"], ["Age"], ["Renal Cell Carcinoma", "", "", "", "", ""], ["rs11708581", "Subjects<65", "679\\157\\5", "639\\196\\15", "Dom", "0.72(0.57-0.91)", "0.0065"], ["", "Subjects≥65", "349\\94\\4", "343\\99\\3", "Dom", "0.92(0.66-1.27)", "0.60"], ["rs390802", "Subjects<65", "601\\226\\18", "552\\265\\32", "Dom", "0.77(0.62-0.95)", "0.014"], ["", "Subjects≥65", "317\\114\\16", "309\\135\\3", "Dom", "0.90(0.67-1.21)", "0.47"], ["Lung", "", "", "", "", "", ""], ["rs12163565", "Subjects<65", "1103\\584\\72", "1138\\554\\72", "Dom", "1.07(0.93-1.23)", "0.32"], ["", "Subjects≥65", "956\\489\\63", "984\\446\\57", "Dom", "1.13(0.97-1.31)", "0.12"]], "row_count": 28, "column_count": 7, "numeric_cells": 88, "header_rows": 1, "locator": "section[5]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:29088836:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:19671cf81cf94399b0fc4ae16ab7584b1f2186209ab5ad77e7b8ea540d536eed", "bytes": 751, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#T4", "version": null, "note": "eQTL analysis on the effect of Proxy SNPs on BAP1 expression level for renal cell carcinoma using data downloaded from TCGA", "structure": {"pmcid": "PMC5650391", "section_index": 6, "section_title": "eQTL analysis", "row_count": 8, "column_count": 6}, "table": {"label": "Table 4", "caption": "eQTL analysis on the effect of Proxy SNPs on BAP1 expression level for renal cell carcinoma using data downloaded from TCGA", "rows": [["Proxy SNP", "r2", "SNP of interest", "Coefficient", "Standard error", "P-value"], ["rs1769", "0.94", "rs11708581", "-0.062", "0.042", "0.142"], ["rs6793317", "0.9", "rs11708581", "-0.079", "0.040", "0.051"], ["rs17052053", "0.9", "rs11708581", "-0.113", "0.041", "0.006"], ["rs11713914", "1.0", "rs11708581", "-0.084", "0.042", "0.050"], ["rs6763882", "0.93", "rs390802", "-0.070", "0.038", "0.067"], ["rs11714402", "0.98", "rs390802", "-0.086", "0.038", "0.023"], ["rs123602", "0.98", "rs390802", "-0.050", "0.041", "0.222"]], "row_count": 8, "column_count": 6, "numeric_cells": 42, "header_rows": 1, "locator": "section[6]/table-wrap[1]#T4"}}, {"id": "asset:table:pmid:29088836:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3c4819e47406ff792c17480b6a98387dee40f687df8f3c08cf00937aeffcbd52", "bytes": 600, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T5", "version": null, "note": "Genotyped genetic variants for BAP1", "structure": {"pmcid": "PMC5650391", "section_index": 11, "section_title": "SNP selection and genotyping", "row_count": 7, "column_count": 5}, "table": {"label": "Table 5", "caption": "Genotyped genetic variants for BAP1", "rows": [["SNP", "Chromosome (hg36)", "Position", "Nucleotide change", "MAF*"], ["rs11708581", "chr3: 52428988", "3’ Flanking", "C>A", "0.05"], ["rs12163565", "chr3: 52430526", "3’ Flanking", "G>A", "0.17"], ["rs390802", "chr3: 52431671", "3’ Flanking", "G>A", "0.13"], ["rs123598", "chr3: 52435860", "3’ UTR", "G>A", "0.03"], ["rs56238158", "chr3: 52439302", "Glu>Lys", "C>T", "0.13"], ["rs13094687", "chr3: 52450043", "5’ Flanking", "A>G", "0.29"]], "row_count": 7, "column_count": 5, "numeric_cells": 24, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T5"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types."}}, {"id": "method-2", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "χ2"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "chi_square_test", "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["glm_logit_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: logistic."}, "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": ["Data on renal clear cell carcinoma were downloaded from The Cancer Genome Atlas (TCGA, dbGaP Study Accession: phs000178.v9.p8, data portal: https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp). Expression data (RNA-seq) and methylation (HumanMethylation450 chip) were measured in tumor samples, somatic copy number was inferred from the tumor samples and paired normal controls (Affymetrix SNP 6.0 platform), and genotyping data were measured from blood derived DNA samples (Affymetrix SNP 6.0 platform)."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["glm_logit_fit"], "assets": ["source:pmid:29088836", "asset:table:pmid:29088836:1", "asset:table:pmid:29088836:2", "asset:table:pmid:29088836:3", "asset:table:pmid:29088836:4", "asset:table:pmid:29088836:5"], "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": "2026-10-31T18:32:37Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 88891, "completion_tokens": 3208, "cached_tokens": 1816}}, "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:29088836", "type": "paper", "label": "pmid:29088836"}, {"id": "source:pmid:29088836", "type": "manuscript", "label": "PMID 29088836 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29088836", "type": "paper", "label": "pmid:29088836"}, {"id": "source:pmid:29088836", "type": "manuscript", "label": "PMID 29088836 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29088836", "type": "extraction", "used": ["source:pmid:29088836"], "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:29088836", "parent_hash": "sha256:c2618e6783b782471c9c2666e55d2939aba38c04e523986df935a37789aa147c", "fork_of": null, "generation": 5}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "chip_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["rk, DNAse clusters, and transcription factor ChIP-seq plots in Supplementary Figure 1 were generat"], "order_basis": "paper_text_order:2420", "id": "assay:1"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["glm_logit_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types."], "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":"2026-11-04T03:16:30+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}}}