{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30539787", "kind": "science-record", "revision": 8, "content_hash": "sha256:daa17524d7c2b8fd5f1e38ddda17106b7f4a980ee3eaaedfa736911f245f946a", "created_at": "2026-11-01T15:40:39Z", "updated_at": "2026-11-01T22:43:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Enhancer of Zeste Homologue 2 Inhibition Attenuates TGF-β Dependent Hepatic Stellate Cell Activation and Liver Fibrosis.", "doi": "10.1016/j.jcmgh.2018.09.005", "pmid": "30539787", "authors": ["Rosa Martin-Mateos", "Thiago M De Assuncao", "Juan Pablo Arab", "Nidhi Jalan-Sakrikar", "Usman Yaqoob", "Thomas Greuter", "Vikas K Verma", "Angela J Mathison", "Sheng Cao", "Gwen Lomberk", "Philippe Mathurin", "Raul Urrutia", "Robert C Huebert", "Vijay H Shah"], "journal": "Cellular and molecular gastroenterology and hepatology", "year": 2019, "abstract": "BACKGROUND & AIMS: Transdifferentiation of hepatic stellate cells (HSCs) into myofibroblasts is a key event in the pathogenesis of liver fibrosis. Transforming growth factor β (TGF-β) and platelet-derived growth factor (PDGF) are canonical HSC activators after liver injury. The aim of this study was to analyze the epigenetic modulators that differentially control TGF-β and PDGF signaling pathways.\nMETHODS: We performed a transcriptomic comparison of HSCs treated with TGF-β or PDGF-BB using RNA sequencing. Among the targets that distinguish these 2 pathways, we focused on the histone methyltransferase class of epigenetic modulators.\nRESULTS: Enhancer of zeste homolog 2 (EZH2) was expressed differentially, showing significant up-regulation in HSCs activated with TGF-β but not with PDGF-BB. Indeed, EZH2 inhibition using either a pharmacologic (GSK-503) or a genetic (small interfering RNA) approach caused a significant attenuation of TGF-β-induced fibronectin, collagen 1α1, and α-smooth muscle actin, both at messenger RNA and protein levels. Conversely, adenoviral overexpression of EZH2 in HSCs resulted in a significant stimulation of fibronectin protein and messenger RNA levels in TGF-β-treated cells. Finally, we conducted in vivo experiments with mice chronically treated with carbon tetrachloride or bile duct ligation. Administration of GSK-503 to mice receiving either carbon tetrachloride or bile duct ligation led to attenuated fibrosis as assessed by Trichrome and Sirius red stains, hydroxyproline, and α-smooth muscle actin/collagen protein assays.\nCONCLUSIONS: TGF-β and PDGF share redundant and distinct transcriptomic targets, with the former predominating in HSC activation. The EZH2 histone methyltransferase is preferentially involved in the TGF-β as opposed to the PDGF signaling pathway. Inhibition of EZH2 attenuates fibrogenic gene transcription in TGF-β-treated HSCs and reduces liver fibrosis in vivo. The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE119606 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119606).", "claims": [{"id": "claim-method", "statement": "Analysis of variance with Bonferroni post-test, nonparametric 2-tailed t test (Mann–Whitney), or paired t test for cell culture experiments were used to assess the statistical significance between groups as appropriate with GraphPad Prism 5 software (GraphPad Software, Inc, La Jolla, CA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30539787", "locator": "sections[26] \"Statistical Analysis\" paragraph 2", "quote": "Analysis of variance with Bonferroni post-test, nonparametric 2-tailed t test (Mann–Whitney), or paired t test for cell culture experiments were used to assess the statistical significance between groups as appropriate with GraphPad Prism 5 software (GraphPad Software, Inc, La Jolla, CA)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE119606 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119606)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30539787", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE119606 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119606)"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30539787"], "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:GSE119606"], "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:GSE119606"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30539787", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.jcmgh.2018.09.005", "sha256": "sha256:a416ea91320fde52ec26f851ac7e1202a377d0b6889e023c200edf2b2df26bfe", "bytes": 54232, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.jcmgh.2018.09.005", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6282644", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE119606", "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=GSE119606", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE119606", "version": null, "note": "The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE119606 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119606)", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE119606 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119606)", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3378746", "GSM3378747", "GSM3378748", "GSM3378749", "GSM3378750", "GSM3378751", "GSM3378752", "GSM3378753", "GSM3378754", "GSM3378755", "GSM3378756", "GSM3378757", "GSM3378758", "GSM3378759", "GSM3378760"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "21290", "taxon": "Homo sapiens", "title": "Inhibition of Enhancer of Zeste Homologue 2 attenuates TGF-β dependent hepatic stellate cell activation and liver fibrosis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30539787:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7ea777511e6d506c2689eb85534050cb90081fac7114e176d0508033bc7ed9b6", "bytes": 1204, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#tbl1", "version": null, "note": "Alphabetical List of Genes Regulated by Both TGF-β and PDGF-BB", "structure": {"pmcid": "PMC6282644", "section_index": 7, "section_title": "TGF-β Shares Overlapping Targets With PDGF but Has a More Dominant Role in HSC Activation", "row_count": 23, "column_count": 5}, "table": {"label": "Table 1", "caption": "Alphabetical List of Genes Regulated by Both TGF-β and PDGF-BB", "rows": [["ADM", "DKK1", "HES4", "NFATC2", "RAP1GAP2"], ["AMOTL2", "E2F7", "HEYL", "NIPAL4", "RASD1"], ["ANGPTL4", "EFR3B", "HOXB-AS2", "NKX3-1", "RHBDL3"], ["ANKRD33B", "EGR3", "IFIT2", "NPTX1", "RHOB"], ["ARAP2", "ELFN1", "IFNE", "NR4A1", "RPL39P5"], ["AXIN2", "ENC1", "IL6", "NR4A3", "RRAD"], ["BBC3", "EPHB3", "IL11", "OLFM2", "RUNX1T1"], ["BMF", "ESM1", "INHBA", "PCDH1", "SCG2"], ["BMP2", "FAM131B", "KCNG1", "PDGFA", "SEMA7A"], ["BMP4", "FAM196A", "KCNN4", "PDGFB", "SPDL1"], ["C3orf52", "FAM196B", "KIAA1644", "PGBD5", "SPHK1"], ["C8orf4", "FBXO32", "KIT", "PITPNM3", "SPRY2"], ["CACNA1G", "FGF18", "KREMEN2", "PKP1", "STC1"], ["CARMIL2", "FGFR3", "LIF", "PLAUR", "TAGLN3"], ["CCNG2", "FOSB", "LOC401472", "PLCH2", "TCF7"], ["CEBPD", "GAL", "LOC541472", "PLEKHF1", "TFPI2"], ["CECR6", "GAS1", "LOC105376292", "PNP", "TNFAIP8L3"], ["CLDN4", "GCSAM", "LRRC8C", "PNRC1", "TRAF1"], ["CNKSR3", "GEM", "LURAP1L", "PODXL", "WNT7B"], ["CREBRF", "GFPT2", "MGC20647", "PTCH1", "ZNF365"], ["CTTNBP2", "GPR3", "MIR17HG", "PTGS2", ""], ["CXCL8", "GREM2", "MMP1", "PTHLH", ""], ["DDIT4", "HBEGF", "NFATC1", "PTPRE", ""]], "row_count": 23, "column_count": 5, "numeric_cells": 17, "header_rows": 0, "locator": "section[7]/table-wrap[1]#tbl1"}}, {"id": "asset:table:pmid:30539787:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8db08eaa5992e4aef7a07d78571d1044c8b16326049021989f504dcec6cc1d8a", "bytes": 1328, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#tbl2", "version": null, "note": "Mice and Human Primer Sequences", "structure": {"pmcid": "PMC6282644", "section_index": 17, "section_title": "Quantitative reverse-transcription polymerase chain reaction", "row_count": 22, "column_count": 3}, "table": {"label": "Table 2", "caption": "Mice and Human Primer Sequences", "rows": [["h EZH2", "Forward", "5′-CCCTGACCTCTGTCTTACTTGTGGA-3′"], ["Reverse", "3′-ACGTCAGATGGTGCCAGAAATA-3′"], ["h Fibronectin", "Forward", "5’-GATAAATCAACAGTGGGAGC-3’"], ["Reverse", "5’-CCCAGATCATGGAGTCTTTA-3’"], ["h α-SMA", "Forward", "5’-GACAGCTACGTGGGTGACGAA-3’"], ["Reverse", "5’-TTTTCCATGTCGTCCCAGTTG-3’"], ["h Collagen 1α1", "Forward", "5’-CCCGGGTTTCAGAGACAACTTC-3’"], ["Reverse", "5’-TCCACATGCTTTATTCCAGACATC-3’"], ["h GAPDH", "Forward", "5’-CCAGGGCTGCTTTTAACTCT-3’"], ["Reverse", "5’-GGACTCCACGACGTACTCA-3’"], ["m β-actin", "Forward", "5’-AGAGGGAAATCGTGCGTGAC-3’"], ["Reverse", "5’-CAATAGTGATGACCTGGCCGT-3’"], ["m Collagen 1α1", "Forward", "5’-GAGCGGAGAGTACTGGATCG-3’"], ["Reverse", "5’-GCTTCTTTTCCTTGGGGTTC-3’"], ["m EZH2", "Forward", "5’-TCCCGTTAAAGACCCTGAATG-3’"], ["Reverse", "5’-TGAAAGTGCCATCCTGATCC-3’"], ["m Fibronectin", "Forward", "5’-GTGGCTGCCTTCAACTTCTC-3’"], ["Reverse", "5’-GTGGGTTGCAAACCTTCAAT-3’"], ["m α-SMA", "Forward", "5’-AAACAGGAATACGACGAAG-3’"], ["Reverse", "5’-CAGGAATGATTTGGAAAGGA-3’"], ["m EZH2", "Forward", "5’-TCCCGTTAAAGACCCTGAATG-3’"], ["Reverse", "5’-TGAAAGTGCCATCCTGATCC-3’"]], "row_count": 22, "column_count": 3, "numeric_cells": 24, "header_rows": 0, "locator": "section[17]/table-wrap[1]#tbl2"}}, {"id": "asset:table:pmid:30539787:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1d00632ad30f25c9ac9d50ec2f6fc074b11557c6bb0abcba810a7f0b8114333c", "bytes": 512, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#tbl3", "version": null, "note": "Antibodies Used in Western Blot Analysis", "structure": {"pmcid": "PMC6282644", "section_index": 18, "section_title": "Western blot analysis", "row_count": 9, "column_count": 2}, "table": {"label": "Table 3", "caption": "Antibodies Used in Western Blot Analysis", "rows": [["Primary antibody", "Company and product number"], ["EZH2", "Cell Signaling 5246"], ["H3K27me3", "Abcam Ab6147"], ["GAPDH", "Invitrogen AM4300"], ["Fibronectin", "Santa Cruz sc-9068"], ["HSC 70", "Santa Cruz sc-7298"], ["Collagen 1", "Southern Biotech (Birmingham, AL) 1310-01"], ["α-SMA", "Abcam ab5694"], ["Histone 3", "Abcam ab1791"]], "row_count": 9, "column_count": 2, "numeric_cells": 12, "header_rows": 1, "locator": "section[18]/table-wrap[1]#tbl3"}}], "gaps": ["asset:data:geo:GSE119606 not downloaded", "asset:data:geo:GSE119606 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Analysis of variance with Bonferroni post-test, nonparametric 2-tailed t test (Mann–Whitney), or paired t test for cell culture experiments were used to assess the statistical significance between groups as appropriate with GraphPad Prism 5 software (GraphPad Software, Inc, La Jolla, CA)."}}], "targets": [], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["GSE119606"], "resolved_accessions": ["GSE119606"], "statements": ["The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE119606 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119606)"], "basis": "The paper names GSE119606 in NCBI's Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:30539787", "data:geo:GSE119606", "asset:table:pmid:30539787:1", "asset:table:pmid:30539787:2", "asset:table:pmid:30539787:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE119606"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 45829, "completion_tokens": 1175, "cached_tokens": 15496}}, "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:30539787", "type": "paper", "label": "pmid:30539787"}, {"id": "source:pmid:30539787", "type": "manuscript", "label": "PMID 30539787 full text"}, {"id": "data:geo:GSE119606", "type": "dataset", "label": "GEO GSE119606"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30539787", "type": "paper", "label": "pmid:30539787"}, {"id": "source:pmid:30539787", "type": "manuscript", "label": "PMID 30539787 full text"}, {"id": "data:geo:GSE119606", "type": "dataset", "label": "GEO GSE119606"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30539787", "type": "extraction", "used": ["source:pmid:30539787"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE119606", "type": "accession_resolution", "used": ["data:geo:GSE119606"], "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:30539787", "parent_hash": "sha256:8269bfb2d2247f01f1849b51d0d55eea1ce1cac94c68f4f95a0b23ad060761c1", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE119606 licence not read", "asset:data:geo:GSE119606 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["of HSCs treated with TGF-β or PDGF-BB using RNA sequencing. Among the targets that distinguish these 2", "signaling pathways. METHODS: We performed a transcriptomic comparison of HSCs treated with TGF-β or PDG", "TGF-β and PDGF share redundant and distinct transcriptomic targets, with the former predominating in HS"], "order_basis": "paper_text_order:502", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["n TGF-β-treated cells. Finally, we conducted in vivo experiments with mice chronically treated wi", "GF-β-treated HSCs and reduces liver fibrosis in vivo. The data discussed in this publication have"], "order_basis": "paper_text_order:1316", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["Sigma-Aldrich) (10 ng/mL) for 48 hours. All cell lines were maintained under standard tissue culture conditions (37"], "order_basis": "paper_text_order:2774", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Analysis of variance with Bonferroni post-test, nonparametric 2-tailed t test (Mann–Whitney), or paired t test for cell culture experiments were used to assess the statistical significance between groups as appropriate with GraphPad Prism 5 software (GraphPad Software, Inc, La Jolla, CA)."], "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":"2026-11-04T03:35:42+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}}}