{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28983581", "kind": "science-record", "revision": 6, "content_hash": "sha256:991be01ee9b53b0224f1aa2c762d4147b53be004fe92e1dee66bf7f6041485d0", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T21:59:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of fibroblasts exposed to TGF‑β at the early proliferation phase of wound repair.", "doi": "10.3892/mmr.2017.7619", "pmid": "28983581", "authors": ["Bobin Mi", "Guohui Liu", "Wu Zhou", "Huijuan Lv", "Kun Zha", "Yi Liu", "Qipeng Wu", "Jing Liu"], "journal": "Molecular medicine reports", "year": 2017, "abstract": "The aim of the current study was to identify gene signatures during the early proliferation stage of wound repair and the effect of TGF‑β on fibroblasts and reveal their potential mechanisms. The gene expression profiles of GSE79621 and GSE27165 were obtained from GEO database. Differentially expressed genes (DEGs) were identified using Morpheus and co‑expressed DEGs were selected using Venn Diagram. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Protein‑protein interaction (PPI) networks of the DEGs were constructed using Cytoscape software. PPI interaction network was divided into subnetworks using the MCODE algorithm and the function of the top one module was analyzed using DAVID. The results revealed that upregulated DEGs were significantly enriched in biological process, including the Arp2/3 complex‑mediated actin nucleation, positive regulation of hyaluronan cable assembly, purine nucleobase biosynthetic process, de novo inosine monophosphate biosynthetic process, positive regulation of epithelial cell proliferation, whereas the downregulated DEGs were enriched in the regulation of blood pressure, negative regulation of cell proliferation, ossification, negative regulation of gene expression and type I interferon signaling pathway. KEGG pathway analysis showed that the upregulated DEGs were enriched in shigellosis, pathogenic Escherichia coli infection, the mitogen‑activated protein kinase signaling pathway, Ras signaling pathway and bacterial invasion of epithelial cells. The downregulated DEGs were enriched in systemic lupus erythematosus, lysosome, arachidonic acid metabolism, thyroid cancer and allograft rejection. The top 10 hub genes were identified from the PPI network. The top module analysis revealed that the included genes were involved in ion channel, neuroactive ligand‑receptor interaction pathway, purine metabolism and intestinal immune network for IgA production pathway. The functional analysis revealed that TGF‑β may promote fibroblast migration and proliferation and defend against microorganisms at the early proliferation stage of wound repair. Furthermore, these results may provide references for chronic wound repair.", "claims": [{"id": "claim-method", "statement": "The data was processed using web-based tool Morpheus (https://software.broadinstitute.org/morpheus/), which is a matrix visualization and analysis platform designed to support visual data exploration.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28983581", "locator": "sections[5] \"Identification of DEGs\" paragraph 2", "quote": "The data was processed using web-based tool Morpheus (https://software.broadinstitute.org/morpheus/), which is a matrix visualization and analysis platform designed to support visual data exploration."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression omnibus (GEO; www.ncbi.nlm.nih.gov/geo) contains original submitter-supplied records and curated DataSets, which is freely available to users. Two gene expression profiles (GSE79621 and GSE27165) were obtained from the GEO database. Data of fibroblast samples and TGF-β 24 h treated fibroblasts samples from the two gene expression profiles. The GSE79621 contained 3 fibroblast samples and 3TGF-β 24 h-treated fibroblast samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28983581", "locator": "sections[4] \"Microarray data\" paragraph 2", "quote": "Gene expression omnibus (GEO; www.ncbi.nlm.nih.gov/geo) contains original submitter-supplied records and curated DataSets, which is freely available to users. Two gene expression profiles (GSE79621 and GSE27165) were obtained from the GEO database. Data of fibroblast samples and TGF-β 24 h treated fibroblasts samples from the two gene expression profiles. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE27165"], "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:GSE27165"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28983581", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/mmr.2017.7619", "sha256": "sha256:2037d02299c59c325b415d41c03b2fa0f1000ee106e896c6ae2c6a8928287ee9", "bytes": 37195, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/mmr.2017.7619", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5779900", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE27165", "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=GSE27165", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27165", "version": null, "note": "Gene expression omnibus (GEO; www.ncbi.nlm.nih.gov/geo) contains original submitter-supplied records and curated DataSets, which is freely available to users. 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Top 5 terms were selected according to P-value when more than five terms enriched terms were identified in each category.", "structure": {"pmcid": "PMC5779900", "section_index": 12, "section_title": "KEGG pathway analysis", "row_count": 17, "column_count": 5}, "table": {"label": "Table II.", "caption": "KEGG pathway analysis of upregulated and downregulated differentially expressed genes. Top 5 terms were selected according to P-value when more than five terms enriched terms were identified in each category.", "rows": [["A, Upregulated"], [""], ["Pathway ID", "Name", "Count", "P-value", "Genes"], ["hsa05131", "Shigellosis", "8", "5.30×10−4", "ACTB, ARPC2, NFKBIB, ARPC5L, ARPC4, MAPK11, MAPK10, FBXW11"], ["hsa05130", "Pathogenic Escherichia coli infection", "6", "0.005446999", "ACTB, TUBB, ARPC2, ARPC5L, TUBA4A, ARPC4"], ["hsa04010", "MAPK signaling pathway", "13", "0.011844961", "NTF3, MRAS, MAPK11, MAPK10, ARRB2, RASGRP1, RASGRP2, PRKACB, FGF1, MYC, GADD45A, RASA1, NFATC1"], ["hsa04014", "Ras signaling pathway", "12", "0.012462871", "LAT, GRIN2B, MRAS, HTR7, RASGRP1, VEGFA, RASGRP2, GNB4, PRKACB, MAPK10, FGF1, RASA1"], ["hsa05100", "Bacterial invasion of epithelial cells", "6", "0.030311184", "ACTB, ARPC2, ARPC5L, ARPC4, CD2AP, FN1"], [""], ["B, Downregulated"], ["Pathway ID", "Name", "Count", "P-value", "Genes"], [""], ["hsa05322", "Systemic lupus erythematosus", "10", "0.006763183", "HIST2H2AA3, HIST1H2AC, HIST1H2BD, HIST1H2BK, HIST2H2BE, HIST2H2AC, HLA-DPA1, C1R, C1S, CD40"], ["hsa04142", "Lysosome", "9", "0.011440506", "CTSK, LAMP2, TPP1, GUSB, SMPD1, PPT2, NEU1, ATP6V0A4, IDUA"], ["hsa00590", "Arachidonic acid metabolism", "6", "0.019902025", "PLA2G4A, TBXAS1, PTGS1, EPHX2, LTA4H, PLA2G4C"], ["hsa05216", "Thyroid cancer", "4", "0.036016354", "TCF7, RXRA, TFG, TCF7L1"], ["hsa05330", "Allograft rejection", "4", "0.066232041", "HLA-C, HLA-DPA1, HLA-B, CD40"]], "row_count": 17, "column_count": 5, "numeric_cells": 35, "header_rows": 3, "locator": "section[12]/table-wrap[1]#tII-mmr-16-06-8146"}}, {"id": "asset:table:pmid:28983581:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:71073787c091551af75de0aca22dd8bdaee384758927a53d43bdf0f6270e1327", "bytes": 850, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tIII-mmr-16-06-8146", "version": null, "note": "Degree of top 10 genes.", "structure": {"pmcid": "PMC5779900", "section_index": 13, "section_title": "PPI network construction and module analysis", "row_count": 11, "column_count": 4}, "table": {"label": "Table III.", "caption": "Degree of top 10 genes.", "rows": [["Gene ID", "Gene name", "Degree", "Expression"], ["GAPDH", "Glyceraldehyde-3-phosphate dehydrogenase", "83", "Upregulation"], ["MYC", "Myc proto-oncogene protein", "55", "Upregulation"], ["CDK1", "Cyclin-dependent kinase 1", "51", "Downregulation"], ["ACTB", "Actin, cytoplasmic 1", "50", "Upregulation"], ["APP", "Amyloid beta A4 protein", "40", "Downregulation"], ["PRKACB", "cAMP-dependent protein kinase catalytic subunit beta", "36", "Upregulation"], ["MAKP11", "Mitogen-activated protein kinase 11", "35", "Upregulation"], ["ACACB", "Acetyl-CoA carboxylase 2", "34", "Downregulation"], ["HSPA4", "Heat shock 70 kDa protein 4", "31", "Upregulation"], ["CAT", "Catalase", "31", "Downregulation"]], "row_count": 11, "column_count": 4, "numeric_cells": 17, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tIII-mmr-16-06-8146"}}, {"id": "asset:table:pmid:28983581:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f8b102316a40b4d8f99ea68fcbc38f640dfd13c7d61eaf4a27028e72fd08d8e1", "bytes": 1012, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#tIV-mmr-16-06-8146", "version": null, "note": "Six modules from the protein-protein interaction network satisfied the criteria of MCODE scores ≥4 and number of nodes >4.", "structure": {"pmcid": "PMC5779900", "section_index": 13, "section_title": "PPI network construction and module analysis", "row_count": 7, "column_count": 5}, "table": {"label": "Table IV.", "caption": "Six modules from the protein-protein interaction network satisfied the criteria of MCODE scores ≥4 and number of nodes >4.", "rows": [["Cluster", "Score", "Nodes", "Edges", "Node IDs"], ["1", "6.353", "35", "108", "FXYD1, ANO1, FXYD3, CD34, POLR3A, GCH1, GNA14, CCR2, NME4, EDNRA, NME2, GUCY1A3, GUCY1A2, PTGER3, PROKR1, HDAC9, TNFSF13B, TUBA4A, DNAJC10, CCT3, GLRB, GLRA1, IARS, CLIC4, CXCL12, CXCR4, RAD51C, GRM7, F2R, RAD51, GAPDH, MKKS, APP, SAA1, ATF3"], ["2", "4.8", "6", "12", "MRAS, LRRC2, FMOD, RAP2C, MST4, PDE7B"], ["3", "4.5", "9", "18", "HLA-B, IRF4, GLDC, ACACB, OAS3, GART, PMPCB, IFIT3, HLA-C"], ["4", "4.5", "5", "9", "WDR4, CECR1, WDR12, PUS1, PUS7"], ["5", "4.3", "21", "43", "MYC, DHX9, MDM2, MCL1, VAMP1, YWHAG, RABL6, UPF2, STX16, TUBB, NUDT21, RAB6A, NSF, RPL37, RPL22, TUBB4Q, PHF5A, ACTB, VAMP4, STX6, AR"], ["6", "4", "4", "6", "COL6A2, COL13A1, COL4A4, COL11A1"]], "row_count": 7, "column_count": 5, "numeric_cells": 28, "header_rows": 1, "locator": "section[13]/table-wrap[2]#tIV-mmr-16-06-8146"}}, {"id": "asset:table:pmid:28983581:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fff161b4992fad501e0c724cdd2ebb7367a659dd15d145f570b4c0dde20e3f2e", "bytes": 1508, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[3]#tV-mmr-16-06-8146", "version": null, "note": "Functional and pathway enrichment analysis of the genes in module. Top 3 terms were selected according to P-value when more than 3 terms enriched terms were identified in each category.", "structure": {"pmcid": "PMC5779900", "section_index": 13, "section_title": "PPI network construction and module analysis", "row_count": 22, "column_count": 5}, "table": {"label": "Table V.", "caption": "Functional and pathway enrichment analysis of the genes in module. Top 3 terms were selected according to P-value when more than 3 terms enriched terms were identified in each category.", "rows": [["A, Biological processes"], [""], ["Term", "Name", "Count", "P-value", "Genes"], ["GO:1902476", "Chloride transmembrane transport", "6", "1.15×10−6", "FXYD1, GLRB, FXYD3, GLRA1, CLIC4, ANO1"], ["GO:0006821", "Chloride transport", "5", "1.22×10−6", "FXYD1, FXYD3, GLRA1, CLIC4, ANO1"], ["GO:0007204", "Positive regulation of cytosolic calcium ion concentration", "6", "8.60×10−6", "EDNRA, PTGER3, CXCR4, SAA1, CCR2, F2R"], [""], ["B, Molecular functions"], [""], ["Term", "Name", "Count", "P-value", "Genes"], [""], ["GO:0005254", "Chloride channel activity", "4", "2.02×10−4", "FXYD1, FXYD3, CLIC4, ANO1"], ["GO:0005525", "GTP binding", "5", "0.007953298", "GNA14, GUCY1A2, GUCY1A3, TUBA4A, GCH1"], ["GO:0016934", "Extracellular-glycine-gated chloride channel activity", "2", "0.010379054", "GLRB, GLRA1"], [""], ["C, KEGG pathways"], [""], ["Term", "Name", "Count", "P-value", "Genes"], [""], ["hsa04080", "Neuroactive ligand-receptor interaction", "6", "0.003899897", "EDNRA, GLRB, PTGER3, GLRA1, GRM7, F2R"], ["hsa00230", "Purine metabolism", "5", "0.00451383", "NME4, NME2, GUCY1A2, GUCY1A3, POLR3A"], ["hsa04672", "Intestinal immune network for IgA production", "3", "0.014264846", "TNFSF13B, CXCR4, CXCL12"]], "row_count": 22, "column_count": 5, "numeric_cells": 29, "header_rows": 3, "locator": "section[13]/table-wrap[3]#tV-mmr-16-06-8146"}}], "gaps": ["asset:data:geo:GSE27165 not downloaded", "asset:data:geo:GSE27165 licence not read", "asset:data:geo:GSE79621 not downloaded", "asset:data:geo:GSE79621 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "Morpheus", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The data was processed using web-based tool Morpheus (https://software.broadinstitute.org/morpheus/), which is a matrix visualization and analysis platform designed to support visual data exploration."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE79621", "GSE27165"], "resolved_accessions": ["GSE79621", "GSE27165"], "statements": ["Gene expression omnibus (GEO; www.ncbi.nlm.nih.gov/geo) contains original submitter-supplied records and curated DataSets, which is freely available to users. Two gene expression profiles (GSE79621 and GSE27165) were obtained from the GEO database. Data of fibroblast samples and TGF-β 24 h treated fibroblasts samples from the two gene expression profiles. The GSE79621 contained 3 fibroblast samples and 3TGF-β 24 h-treated fibroblast samples."], "basis": "The paper names GSE79621, GSE27165 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": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:28983581", "data:geo:GSE27165", "asset:table:pmid:28983581:1", "asset:table:pmid:28983581:2", "asset:table:pmid:28983581:3", "asset:table:pmid:28983581:4", "asset:table:pmid:28983581:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE27165"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:10:20Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 29271, "completion_tokens": 1303, "cached_tokens": 656}}, "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:28983581", "type": "paper", "label": "pmid:28983581"}, {"id": "source:pmid:28983581", "type": "manuscript", "label": "PMID 28983581 full text"}, {"id": "data:geo:GSE27165", "type": "dataset", "label": "GEO GSE27165"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28983581", "type": "paper", "label": "pmid:28983581"}, {"id": "source:pmid:28983581", "type": "manuscript", "label": "PMID 28983581 full text"}, {"id": "data:geo:GSE27165", "type": "dataset", "label": "GEO GSE27165"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28983581", "type": "extraction", "used": ["source:pmid:28983581"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE27165", "type": "accession_resolution", "used": ["data:geo:GSE27165"], "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:28983581", "parent_hash": "sha256:48b6dbb53b68d3ae177e19bad81e9e441a6d49c2f5f7b0b780ebeeff2141c393", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE27165 licence not read", "asset:data:geo:GSE27165 not downloaded", "asset:data:geo:GSE79621 licence not read", "asset:data:geo:GSE79621 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["PPI"], "order_basis": "analysis_only", "id": "assay:1"}]},"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":"2026-11-04T00:37:34+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}}}