{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28624786", "kind": "science-record", "revision": 9, "content_hash": "sha256:7377b95252794cee72b8bf8f83003ca0e75f34b789f59a78a16348624bbe0e74", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T22:43:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "High expression of GPR116 indicates poor survival outcome and promotes tumor progression in colorectal carcinoma.", "doi": "10.18632/oncotarget.18203", "pmid": "28624786", "authors": ["Li Yang", "Xiao-Lu Lin", "Wei Liang", "Seng-Wang Fu", "Wen-Feng Lin", "Xiao-Qing Tian", "Yun-Jie Gao", "Hao-Yan Chen", "Jun Dai", "Zhi-Zheng Ge"], "journal": "Oncotarget", "year": 2017, "abstract": "Previous studies have found that G-protein-coupled receptor 116 (GPR116) is a regulator of breast cancer metastasis. However, the role of GPR116 in colorectal carcinoma (CRC) carcinogenesis and progression is unknown. In this study, We found GPR116 expression was significantly up-regulated in CRC specimens compared with corresponding non-cancerous tissues. Increased GPR116 expression in CRC was correlated with histological differentiation and distant metastasis. In addition, high expression of GPR116 was significantly associated with poor overall survival of CRC patients, which was also confirmed by GSE14333, GSE17536 and GSE33113 datasets from the Gene Expression Omnibus (GEO). Furthermore, we demonstrated that the ability of proliferation and invasion of CRC cell lines HCT116 and LOVO was markedly reduced after transfected with siRNA-GPR116. Meanwhile, GPR116 may drive EMT in CRC cells through AKT/EKR signaling pathway, resulting in metastasis. Thus, GPR116 may be a novel reliable prognostic indicator and a risk factor in CRC progression.", "claims": [{"id": "claim-method", "statement": "We used the Chi-square test or Fisher's exact test to evaluate the correlation between GPR116 expression and corresponding patients’ clinicopathological parameters.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28624786", "locator": "sections[5] \"Correlation of GPR116 expression with clinicopathological characteristics and prognosis in CRC patients\" paragraph 2", "quote": "We used the Chi-square test or Fisher's exact test to evaluate the correlation between GPR116 expression and corresponding patients’ clinicopathological parameters."}], "state": "complete"}, {"id": "claim-data-access", "statement": "To increase the reliability of this result, we obtained the prognostic significance of GPR116 in GSE14333, GSE17536, and GSE33113 with a total of 197, 177, and 89 cases enrolled from the GEO datasets. We found that high GPR116 protein expression was obviously associated with reduced overall survival time (p=0, 0.03, and 0.001 respectively, Figure 3B-3D).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28624786", "locator": "sections[5] \"Correlation of GPR116 expression with clinicopathological characteristics and prognosis in CRC patients\" paragraph 3", "quote": "To increase the reliability of this result, we obtained the prognostic significance of GPR116 in GSE14333, GSE17536, and GSE33113 with a total of 197, 177, and 89 cases enrolled from the GEO datasets. We found that high GPR116 protein expression was obviously associated with reduced overall survival time (p=0, 0.03, and 0.001 respectively, Figure 3B-3D)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "GPR116 was significantly up-regulated in CRC and high expression predicted unfavorable prognosis; clinicopathological associations were assessed using Chi-square or Fisher’s exact tests, survival with Kaplan–Meier/log-rank and Cox regression analyses, and two-group comparisons with Student’s t-test, using Renji cohort pathology and follow-up data supplemented by Oncomine, TCGA, and GEO datasets.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28624786", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "GPR116 expression was significantly up-regulated in CRC specimens compared with corresponding non-cancerous tissues. Increased GPR116 expression in CRC was correlated with histological differentiation and distant metastasis. In addition, high expression of GPR116 was significantly associated with poor overall survival of CRC patients, which was also confirmed by GSE14333, GSE17536 and GSE33113 datasets from the Gene Expression Omnibus (GEO)."}, {"asset": "source:pmid:28624786", "locator": "sections[5] \"Correlation of GPR116 expression with clinicopathological characteristics and prognosis in CRC patients\" paragraph 2", "quote": "We used the Chi-square test or Fisher's exact test to evaluate the correlation between GPR116 expression and corresponding patients’ clinicopathological parameters."}, {"asset": "source:pmid:28624786", "locator": "sections[5] \"Correlation of GPR116 expression with clinicopathological characteristics and prognosis in CRC patients\" paragraph 5", "quote": "To investigate whether GPR116 expression was an independent prognostic parameter in CRC, we used the Cox regression analysis to determine the effect of each variable on survival."}, {"asset": "source:pmid:28624786", "locator": "sections[12] \"Bioinformatics analysis\" paragraph 2", "quote": "The datasets in Oncomine Cancer Microarray database (https://www.oncomine.org) were used to determine the expression pattern of GPR116 in CRC. The dataset of corresponding clinical data used in this study were downloaded from the Gene Expression Omnibus (GEO)."}, {"asset": "source:pmid:28624786", "locator": "sections[6] \"Biological functions of GPR116 in CRC\" paragraph 2", "quote": "Gene set enrichment analysis (GSEA) was performed in The Cancer Genome Atlas (TCGA) datasets to acquire the biologic functions involved in CRC pathogenesis stratified by the median of GPR116 expression level."}, {"asset": "source:pmid:28624786", "locator": "sections[19] \"Statistical analysis\" paragraph 2", "quote": "Correlation of GPR116 expression with clinicopathologic factors in patients with CRC was evaluated by Chi-square test. Survival curves were generated using the Kaplan–Meier method. The differences between survival curves were calculated by the Log-rank test. The significant impact of parameters on survival was analyzed by Cox proportional hazards model using univariate and multivariate Cox regression analysis. The comparison between two groups was evaluated by Student's t-test."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "GPR116 was significantly up-regulated in CRC and high expression predicted unfavorable prognosis; clinicopathological associations were assessed using Chi-square or Fisher’s exact tests, survival with Kaplan–Meier/log-rank and Cox regression analyses, and two-group comparisons with Student’s t-test, using Renji cohort pathology and follow-up data supplemented by Oncomine, TCGA, and GEO datasets.", "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:28624786"], "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. 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We found that high GPR116 protein expression was obviously associated with reduced overall survival time (p=0, 0.03, and 0.001 respectively, Figure 3B-3D).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "To increase the reliability of this result, we obtained the prognostic significance of GPR116 in GSE14333, GSE17536, and GSE33113 with a total of 197, 177, and 89 cases enrolled from the GEO datasets. 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"52", "28 (53.8)", "24 (46.2)", "0.909"], ["Female", "38", "20 (52.6)", "18 (47.4)", ""], ["Tumor location", "", "", "", ""], ["Ascending", "28", "17 (60.7)", "11 (39.3)", "0.522"], ["Transverse", "20", "9 (45.0)", "11 (55.0)", ""], ["Descending", "16", "10 (62.5)", "6 (37.5)", ""], ["Sigmoid", "26", "12 (46.2)", "14 (53.8)", ""], ["TNM stage (AJCC)", "", "", "", ""], ["Stage I", "5", "0 (0.0)", "5 (100.0)", "0.102"], ["Stage II", "37", "20 (54.1)", "17 (45.9)", ""], ["Stage III", "43", "25 (58.1)", "18 (41.9)", ""], ["Stage IV", "5", "3 (60.0)", "2 (40.0)", ""], ["Size", "", "", "", ""], ["<5cm", "34", "16 (47.1)", "18 (52.9)", "0.353"], ["≥5cm", "56", "32 (57.1)", "24 (42.9)", ""], ["Histological differentiation", "", "", "", ""], ["Well/moderate", "56", "25 (45.5)", "31 (54.5)", "0.034"], ["Poor", "34", "23 (65.7)", "11 (34.3)", ""], ["Lymph node metastasis", "", "", "", ""], ["Absent", "46", "22 (47.8)", "24 (52.2)", "0.284"], ["Present", "44", "26 (59.1)", "18 (40.9)", ""], ["Distant metastasis", "", "", "", ""], ["Absent", "85", "43 (50.6)", "42 (49.4)", "0.031"], ["Present", "5", "5 (100.0)", "0 (0.0)", ""]], "row_count": 31, "column_count": 5, "numeric_cells": 77, "header_rows": 2, "locator": "section[4]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:28624786:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:252e01fee8ef0d734c6c11abc495b14492640f8235f8ebe799d21897dc270f7f", "bytes": 1112, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T2", "version": null, "note": "Univariate and multivariate analysis of prognostic parameters for survival in patients with colorectal carcinoma", "structure": {"pmcid": "PMC5564617", "section_index": 5, "section_title": "Correlation of GPR116 expression with clinicopathological characteristics and prognosis in CRC patients", "row_count": 10, "column_count": 7}, "table": {"label": "Table 2", "caption": "Univariate and multivariate analysis of prognostic parameters for survival in patients with colorectal carcinoma", "rows": [["Prognostic parameter", "Univariate analysis", "Multivariate analysis"], ["HR", "95% CI", "P value", "HR", "95% CI", "P value"], ["Expression of GPR116 (low vs. high)", "2.465", "1.310-4.637", "0.005", "2.693", "1.381-5.255", "0.004"], ["Age (<65 vs. ≥65)", "1.979", "1.025-3.819", "0.042", "2.006", "1.020-3.943", "0.044"], ["Gender (male vs. female)", "0.710", "0.389-1.298", "0.266", "_", "_", "_"], ["Tumor size (<5cm vs. ≥5cm)", "0.842", "0.445-1.596", "0.599", "_", "_", "_"], ["Lymph node metastasis (absent vs. present)", "2.215", "1.192-4.116", "0.012", "1.254", "0.626-2.515", "0.523"], ["Distant metastasis (absent vs. present)", "1.815", "0.711-4.635", "0.213", "_", "_", "_"], ["Tumor location (ascending vs. transverse, descending, sigmoid)", "0.646", "0.340-1.224", "0.180", "_", "_", "_"], ["Histology (well/moderate vs. poor)", "2.080", "1.109-3.903", "0.022", "2.173", "1.036-4.559", "0.040"]], "row_count": 10, "column_count": 7, "numeric_cells": 41, "header_rows": 2, "locator": "section[5]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE14333 not downloaded", "asset:data:geo:GSE14333 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE33113 not downloaded", "asset:data:geo:GSE33113 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "We used the Chi-square test or Fisher's exact test to evaluate the correlation between GPR116 expression and corresponding patients’ clinicopathological parameters."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Student's t-test"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-4", "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": 0.8, "band": "high", "quote": "Log-rank"}}, {"id": "method-5", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}, {"id": "method-6", "family": "contingency_analysis", "specific": "fisher_exact", "label": "Categorical (contingency table) analysis", "dsl_operations": ["contingency_table", "chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Fisher's exact"}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["chi_square_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: chi_square."}, "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": ["GSE14333", "GSE17536", "GSE33113"], "resolved_accessions": ["GSE14333", "GSE17536", "GSE33113"], "statements": ["To increase the reliability of this result, we obtained the prognostic significance of GPR116 in GSE14333, GSE17536, and GSE33113 with a total of 197, 177, and 89 cases enrolled from the GEO datasets. We found that high GPR116 protein expression was obviously associated with reduced overall survival time (p=0, 0.03, and 0.001 respectively, Figure 3B-3D)."], "basis": "The paper names GSE14333, GSE17536, GSE33113 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": ["chi_square_test"], "assets": ["source:pmid:28624786", "data:geo:GSE14333", "asset:table:pmid:28624786:1", "asset:table:pmid:28624786:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14333"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:31:22Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 59140, "completion_tokens": 6900, "cached_tokens": 1832}}, "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:28624786", "type": "paper", "label": "pmid:28624786"}, {"id": "source:pmid:28624786", "type": "manuscript", "label": "PMID 28624786 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28624786", "type": "paper", "label": "pmid:28624786"}, {"id": "source:pmid:28624786", "type": "manuscript", "label": "PMID 28624786 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28624786", "type": "extraction", "used": ["source:pmid:28624786"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14333", "type": "accession_resolution", "used": ["data:geo:GSE14333"], "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:28624786", "parent_hash": "sha256:d77967d3d13cde9f628f1c423820bfab09193c11b4347baab4a4e9b4f677a03d", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE14333 licence not read", "asset:data:geo:GSE14333 not downloaded", "asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE33113 licence not read", "asset:data:geo:GSE33113 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s HCT116 and LOVO was markedly reduced after transfected with siRNA-GPR116. Meanwhile, GPR116 may dri", "was markedly reduced after transfected with siRNA-GPR116. Meanwhile, GPR116 may drive EMT in C", "10% FBS at 37°C in an atmosphere of 5% CO2. Transfection of siRNA was performed using Lipofectamine 2", "ccording to the manufacturer's protocol. The transfection reagent was replaced by complete medium afte"], "order_basis": "paper_text_order:894", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["in CRC according to its mRNA expression and immunohistochemical scoring. Results demonstrated that GPR116 wa", "ROC: receiver operating characteristic; IHC: immunohistochemical. MATERIALS AND METHODS Patients and tissue s", "e analysis according to GPR116 expression by IHC. ROC: receiver operating characteristic; IHC", "IHC. ROC: receiver operating characteristic; IHC: immunohistochemical. MATERIALS AND METHODS"], "order_basis": "paper_text_order:5171", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["CR, and another 6 samples were collected for western blot. This study was approved by the Ethics Commi"], "order_basis": "paper_text_order:7025", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["American Type Culture Collection. They were cultured in RPMI 1640 medium (Gibco, Gaithersburg, MD, U"], "order_basis": "paper_text_order:7463", "id": "assay:4"}, {"role": "analysis", "definition_id": "contingency_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["chi_square_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We used the Chi-square test or Fisher's exact test to evaluate the correlation between GPR116 expression and corresponding patients’ clinicopathological parameters."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]},"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":"2026-11-04T01:20:41+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}}}