{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29556287", "kind": "science-record", "revision": 9, "content_hash": "sha256:c7086a83437fd0b65bc9c3b512c08499eb0fe632f5cf55d692719719051671d1", "created_at": "2026-11-01T15:40:32Z", "updated_at": "2026-11-01T22:43:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Increased mediator complex subunit 15 expression is associated with poor prognosis in hepatocellular carcinoma.", "doi": "10.3892/ol.2018.7820", "pmid": "29556287", "authors": ["Kunyuan Wang", "Chenxi Duan", "Xuejing Zou", "Yang Song", "Wenwen Li", "Lushan Xiao", "Jie Peng", "Liheng Yao", "Qian Long", "Li Liu"], "journal": "Oncology letters", "year": 2018, "abstract": "Mediator complex subunit 15 (MED15) is a coactivator involved in the regulated transcription of RNA polymerase II-dependent genes and serves an oncogenic role in numerous types of cancer. However, the expression and function of MED15 in hepatocellular carcinoma (HCC) remain unknown. In the present study, the aim was to investigate the expression and clinical significance of MED15 in HCC. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical analysis revealed that MED15 mRNA and protein levels were significantly upregulated in HCC tissues compared with those in the corresponding adjacent non-tumor liver tissues. Furthermore, analyzing data from The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) and GSE14520 datasets revealed a significant correlation between MED15 expression and the tumor size (P=0.033), Barcelona Clinic Liver Cancer stage (P=0.031), α-fetoprotein levels (P=0.002) and metastasis risk (P=0.001). Furthermore, patients with high MED15 expression levels had a shorter survival time compared with those with low MED15 expression levels (P<0.05). Univariate and multivariate analyses further revealed that MED15 may be an independent prognostic factor for the overall survival of HCC patients (hazard ratio, 1.762; 95% confidence interval, 1.077-2.882; P<0.05). In addition, MED15 expression was positively associated with hypoxia-inducible factor 1α expression in the TCGA-LIHC and GSE14520 datasets (P<0.01). In conclusion, the data reported in the present study indicated that MED15 is overexpressed in HCC and may represent a novel prognostic biomarker for patients with HCC.", "claims": [{"id": "claim-method", "statement": "Kaplan-Meier and log-rank test analyses were employed to test for an association between MED15 expression and the OS or DFS of the patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29556287", "locator": "sections[16] \"MED15 expression levels predict the clinical outcome of patients with HCC\" paragraph 2", "quote": "Kaplan-Meier and log-rank test analyses were employed to test for an association between MED15 expression and the OS or DFS of the patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In order to investigate the role of MED15 expression in HCC, the current study analyzed the TCGA-LIHC dataset (http://www.cbioportal.org/data_sets.jsp) that contains 331 HCC cases and the GSE14520 dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520) that provides 246 HCC cases (hereafter defined as the TCGA-LIHC and GSE14520 cohorts, respectively). These datasets comprise follow-up information for patients and gene expression data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29556287", "locator": "sections[8] \"TCGA-LIHC and GSE14520 datasets, Oncomine gene expression array\" paragraph 2", "quote": "In order to investigate the role of MED15 expression in HCC, the current study analyzed the TCGA-LIHC dataset (http://www.cbioportal.org/data_sets.jsp) that contains 331 HCC cases and the GSE14520 dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520) that provides 246 HCC cases (hereafter defined as the TCGA-LIHC and GSE14520 cohorts, respectively). These datasets comprise follow-up information for patients and gene expression data."}], "state": "complete"}, {"id": "claim-target-result", "statement": "MED15 mRNA and protein expression were significantly upregulated in HCC tissues, and high MED15 expression was associated with poor prognosis; the study used RT-qPCR and immunohistochemical analysis of tissue specimens and analyzed the TCGA-LIHC and GSE14520 datasets for clinicopathological and survival associations.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29556287", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical analysis revealed that MED15 mRNA and protein levels were significantly upregulated in HCC tissues compared with those in the corresponding adjacent non-tumor liver tissues."}, {"asset": "source:pmid:29556287", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Furthermore, analyzing data from The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) and GSE14520 datasets revealed a significant correlation between MED15 expression and the tumor size (P=0.033), Barcelona Clinic Liver Cancer stage (P=0.031), α-fetoprotein levels (P=0.002) and metastasis risk (P=0.001)."}, {"asset": "source:pmid:29556287", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In conclusion, the data reported in the present study indicated that MED15 is overexpressed in HCC and may represent a novel prognostic biomarker for patients with HCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "MED15 mRNA and protein expression were significantly upregulated in HCC tissues, and high MED15 expression was associated with poor prognosis; the study used RT-qPCR and immunohistochemical analysis of tissue specimens and analyzed the TCGA-LIHC and GSE14520 datasets for clinicopathological and survival associations.", "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:29556287"], "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:GSE14520"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE14520"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29556287", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ol.2018.7820", "sha256": "sha256:c645ea2e7e3cf60ad75f4b62b2153c438a9cb187284f27d6fdf7d9b3a7ea0dc5", "bytes": 36608, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/ol.2018.7820", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5844107", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14520", "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=GSE14520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14520", "version": null, "note": "In order to investigate the role of MED15 expression in HCC, the current study analyzed the TCGA-LIHC dataset (http://www.cbioportal.org/data_sets.jsp) that contains 331 HCC cases and the GSE14520 dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520) that provides 246 HCC cases (hereafter defined as the TCGA-LIHC and GSE14520 cohorts, respectively). 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"section[17]/table-wrap[1]#tIII-ol-0-0-7820", "version": null, "note": "Univariate and multivariate analyses (Cox regression analysis) indicating the association between overall survival and the characteristics of hepatocellular carcinoma patients in The Cancer Genome Atlas-Liver Hepatocellular Carcinoma cohort.", "structure": {"pmcid": "PMC5844107", "section_index": 17, "section_title": "MED15 may be a valuable prognostic marker for patients with HCC", "row_count": 15, "column_count": 7}, "table": {"label": "Table III.", "caption": "Univariate and multivariate analyses (Cox regression analysis) indicating the association between overall survival and the characteristics of hepatocellular carcinoma patients in The Cancer Genome Atlas-Liver Hepatocellular Carcinoma cohort.", "rows": [["Variable", "Univariate analysis", "Multivariate analysis"], ["", "", ""], ["", "HR", "95% CI", "P-value", "HR", "95% CI", "P-value"], ["Sex", "0.754", "0.510–1.114", "0.156", "", "", ""], ["Age (years)", "0.943", "0.574–1.552", "0.819", "", "", ""], ["Family cancer history", "1.298", "0.859–1.961", "0.216", "", "", ""], ["Lymphocyte infiltration", "1.107", "0.770–1.592", "0.582", "", "", ""], ["Vascular tumor cell invasion", "1.016", "0.703–1.469", "0.932", "", "", ""], ["Neoplasm grade", "1.310", "0.883–1.945", "0.180", "", "", ""], ["Pathologic stage", "1.420", "0.922–2.187", "0.112", "", "", ""], ["AFP level (ng/ml)", "1.566", "0.976–2.512", "0.063", "", "", ""], ["Child-Pugh classification grade", "1.548", "0.760–3.151", "0.229", "", "", ""], ["Liver fibrosis Ishak score", "1.059", "0.591–1.898", "0.846", "", "", ""], ["Relapse", "1.052", "0.711–1.556", "0.801", "", "", ""], ["MED15 expression", "1.581", "1.039–2.404", "0.032a", "1.762", "1.077–2.882", "0.024a"]], "row_count": 15, "column_count": 7, "numeric_cells": 42, "header_rows": 3, "locator": "section[17]/table-wrap[1]#tIII-ol-0-0-7820"}}, {"id": "asset:table:pmid:29556287:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e5da25abd6c74f86bb7cc28f664633b258a329e4e58f87b909706ba4fc8a78b6", "bytes": 1279, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[2]#tIV-ol-0-0-7820", "version": null, "note": "Univariate and multivariate analyses (Cox regression analysis) indicating the association between overall survival and the characteristics of hepatocellular carcinoma patients in the GSE14520 cohort.", "structure": {"pmcid": "PMC5844107", "section_index": 17, "section_title": "MED15 may be a valuable prognostic marker for patients with HCC", "row_count": 14, "column_count": 7}, "table": {"label": "Table IV.", "caption": "Univariate and multivariate analyses (Cox regression analysis) indicating the association between overall survival and the characteristics of hepatocellular carcinoma patients in the GSE14520 cohort.", "rows": [["", "Univariate analysis", "Multivariate analysis"], ["", "", ""], ["Variable", "HR", "95% CI", "P-value", "HR", "95% CI", "P-value"], ["Sex", "1.870", "0.907–3.858", "0.090", "", "", ""], ["Age (years)", "0.911", "0.610–1.360", "0.647", "", "", ""], ["No. of tumors", "1.642", "1.057–2.551", "0.027a", "0.389", "0.203–0.745", "0.004a"], ["Tumor size (cm)", "1.954", "1.306–2.924", "0.001a", "", "", "0.493"], ["BCLC staging", "3.357", "2.211–5.096", "<0.001a", "3.615", "1.982–6.593", "<0.001a"], ["TNM staging", "3.084", "1.883–5.053", "<0.001a", "", "", "0.337"], ["AFP level (ng/ml)", "1.710", "1.141–2.562", "0.009a", "", "", "0.589"], ["Cirrhosis", "5.126", "1.263–20.804", "0.022a", "4.456", "1.081–18.367", "0.039"], ["Metastasis risk", "2.281", "1.504–3.459", "<0.001a", "2.41", "1.523–3.814", "0.001a"], ["Relapse", "122.187", "17.008–877.810", "<0.001a", "91.516", "12.664–661.334", "<0.001a"], ["MED15 expression", "1.517", "0.950–2.425", "0.081", "", "", ""]], "row_count": 14, "column_count": 7, "numeric_cells": 54, "header_rows": 3, "locator": "section[17]/table-wrap[2]#tIV-ol-0-0-7820"}}], "gaps": ["asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE14520 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Kaplan-Meier and log-rank test analyses were employed to test for an association between MED15 expression and the OS or DFS of the patients."}}, {"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": "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-4", "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 proportional hazards"}}, {"id": "method-5", "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"}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE14520"], "resolved_accessions": ["GSE14520"], "statements": ["In order to investigate the role of MED15 expression in HCC, the current study analyzed the TCGA-LIHC dataset (http://www.cbioportal.org/data_sets.jsp) that contains 331 HCC cases and the GSE14520 dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520) that provides 246 HCC cases (hereafter defined as the TCGA-LIHC and GSE14520 cohorts, respectively). These datasets comprise follow-up information for patients and gene expression data."], "basis": "The paper names GSE14520 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:29556287", "data:geo:GSE14520", "asset:table:pmid:29556287:1", "asset:table:pmid:29556287:2", "asset:table:pmid:29556287:3", "asset:table:pmid:29556287:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14520"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:05Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 75128, "completion_tokens": 3996, "cached_tokens": 10528}}, "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:29556287", "type": "paper", "label": "pmid:29556287"}, {"id": "source:pmid:29556287", "type": "manuscript", "label": "PMID 29556287 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29556287", "type": "paper", "label": "pmid:29556287"}, {"id": "source:pmid:29556287", "type": "manuscript", "label": "PMID 29556287 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29556287", "type": "extraction", "used": ["source:pmid:29556287"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14520", "type": "accession_resolution", "used": ["data:geo:GSE14520"], "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:29556287", "parent_hash": "sha256:a13b28f004d181770f76d5573f62248b232308e1170ac2348d6d03eef078b0f4", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE14520 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": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tion-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical analysis revealed t", "n-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical analysis revealed t", "sis Student's t-test was used to analyze the RT-qPCR results, while Mann-Whitney U-test was used", "Student's t-test was used to analyze the RT-qPCR results, while Mann-Whitney U-test was used"], "order_basis": "paper_text_order:520", "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": 0.93, "evidence": ["tive polymerase chain reaction (RT-qPCR) and immunohistochemical analysis revealed that MED15 mRNA and protei"], "order_basis": "paper_text_order:533", "id": "assay:2"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["=0.028; Fig. 4B). Furthermore, a comparative microarray analysis of gene expression was performed in"], "order_basis": "paper_text_order:4350", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan-Meier and log-rank test analyses were employed to test for an association between MED15 expression and the OS or DFS of the patients."], "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":"2026-11-04T00:37:57+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}}}