{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29967729", "kind": "science-record", "revision": 6, "content_hash": "sha256:22fca9a8b308bb0a334d5a8c328fb98588c072fdff7497d35c685852e7025cb7", "created_at": "2026-11-01T15:40:35Z", "updated_at": "2026-11-01T21:21:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Pathway analysis identifies altered mitochondrial metabolism, neurotransmission, structural pathways and complement cascade in retina/RPE/ choroid in chick model of form-deprivation myopia.", "doi": "10.7717/peerj.5048", "pmid": "29967729", "authors": ["Loretta Giummarra", "Sheila G Crewther", "Nina Riddell", "Melanie J Murphy", "David P Crewther"], "journal": "PeerJ", "year": 2018, "abstract": "PURPOSE: RNA sequencing analysis has demonstrated bidirectional changes in metabolism, structural and immune pathways during early induction of defocus induced myopia. Thus, the aim of this study was to investigate whether similar gene pathways are also related to the more excessive axial growth, ultrastructural and elemental microanalytic changes seen during the induction and recovery from form-deprivation myopia (FDM) in chicks and predicted by the RIDE model of myopia.\nMETHODS: Archived genomic transcriptome data from the first three days of induction of monocularly occluded form deprived myopia (FDMI) in chicks was obtained from the GEO database (accession # GSE6543) while data from chicks monocularly occluded for 10 days and then given up to 24 h of normal visual recovery (FDMR) were collected. Gene set enrichment analysis (GSEA) software was used to determine enriched pathways during the induction (FDMI) and recovery (FDMR) from FD. Curated gene-sets were obtained from open access sources.\nRESULTS: Clusters of significant changes in mitochondrial energy metabolism, neurotransmission, ion channel transport, G protein coupled receptor signalling, complement cascades and neuron structure and growth were identified during the 10 days of induction of profound myopia and were found to correlate well with change in axial dimensions. Bile acid and bile salt metabolism pathways (cholesterol/lipid metabolism and sodium channel activation) were significantly upregulated during the first 24 h of recovery from 10 days of FDM.\nCONCLUSIONS: The gene pathways altered during induction of FDM are similar to those reported in defocus induced myopia and are established indicators of oxidative stress, osmoregulatory and associated structural changes. These findings are also consistent with the choroidal thinning, axial elongation and hyperosmotic ion distribution patterns across the retina and choroid previously reported in FDM and predicted by RIDE.", "claims": [{"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:The data discussed in this article are available in NCBI’s Gene Expression Omnibus under accession number GSE89325.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29967729", "locator": "sections[32] \"Microarray Data Availability\" paragraph 2", "quote": "The following information was supplied regarding data availability:The data discussed in this article are available in NCBI’s Gene Expression Omnibus under accession number GSE89325."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used Gene Set Enrichment Analysis (GSEA) to compare archived GEO induction data (GSE6543) with newly collected FDMR microarray data, finding pathway changes involving mitochondrial energy metabolism, neurotransmission, ion transport, complement cascades, and bile acid metabolism.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29967729", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Gene set enrichment analysis (GSEA) software was used to determine enriched pathways during the induction (FDMI) and recovery (FDMR) from FD."}, {"asset": "source:pmid:29967729", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Archived genomic transcriptome data from the first three days of induction of monocularly occluded form deprived myopia (FDMI) in chicks was obtained from the GEO database (accession # GSE6543) while data from chicks monocularly occluded for 10 days and then given up to 24 h of normal visual recovery (FDMR) were collected."}, {"asset": "source:pmid:29967729", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Clusters of significant changes in mitochondrial energy metabolism, neurotransmission, ion channel transport, G protein coupled receptor signalling, complement cascades and neuron structure and growth were identified during the 10 days of induction of profound myopia and were found to correlate well with change in axial dimensions. Bile acid and bile salt metabolism pathways (cholesterol/lipid metabolism and sodium channel activation) were significantly upregulated during the first 24 h of recovery from 10 days of FDM."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used Gene Set Enrichment Analysis (GSEA) to compare archived GEO induction data (GSE6543) with newly collected FDMR microarray data, finding pathway changes involving mitochondrial energy metabolism, neurotransmission, ion transport, complement cascades, and bile acid metabolism.", "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:29967729"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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Most genes responding to FD are involved in mitochondrial energy metabolism. The NES reflects the degree to which a set of genes is over-represented at either the top or bottom of a ranked list of genes while also taking into account differences in pathway size (i.e. gene-set size) and is the primary statistic for examining enrichment results, and for comparing results across pathways.", "structure": {"pmcid": "PMC6026464", "section_index": 15, "section_title": "Enrichment analysis for short-term FDM induction", "row_count": 14, "column_count": 5}, "table": {"label": "Table 1", "caption": "Pathways enriched between 6 h and 72 h of FD induction.Mean Normalised Enrichment Score (NES) and false discovery rate (FDR) for the biological pathways identified by GSEA in FD induction. Most genes responding to FD are involved in mitochondrial energy metabolism. The NES reflects the degree to which a set of genes is over-represented at either the top or bottom of a ranked list of genes while also taking into account differences in pathway size (i.e. gene-set size) and is the primary statistic for examining enrichment results, and for comparing results across pathways.", "rows": [["Pathway", "Core genes", "Database", "NES", "FDR"], ["Huntingtons disease", "APAF1, ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5H, ATP5O, BDNF, CASP3, CASP8, CLTA, COX4I1, COX5A, COX6A1, COX6C, COX7A2, COX7A2L, COX7C, COX8A, CYCS, DNAH3, DNAI1, DNAL1, DNALI1, GPX1, HDAC2, IFT57, NDUFA1, NDUFA10, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB4, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, PLCB1, PLCB4, POLR2D, POLR2F, POLR2J, POLR2L, PPID, SDHA, SLC25A4, SLC25A6, SOD2, TAF4, TBP, TBPL1, TFAM, UQCR10, UQCR11, UQCRFS1, UQCRH, VDAC3", "KEGG", "1.76", "0.15"], ["Oxidative phosphorylation", "ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5H, ATP5I, ATP5J2, ATP5O, ATP6V0D2, ATP6V1G1, COX11, COX15, COX17, COX4I1, COX5A, COX6A1, COX6C, COX7A2, COX7A2L, COX7C, COX8A, NDUFA1, NDUFA10, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB4, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, PPA1, PPA2, SDHA, UQCR10, UQCR11, UQCRFS1, UQCRH", "KEGG", "1.81", "0.16"], ["Mitochondrial protein import", "BCS1L, CHCHD4, COX17, DNAJC19, GRPEL1, HSCB, HSPD1, PAM16, PMPCA, PMPCB, SAMM50, SLC25A12, SLC25A4, SLC25A6, TIMM13, TIMM17A, TIMM22, TIMM44, TIMM9, TOMM22, TOMM5, TOMM7", "Reactome", "1.80", "0.16"], ["One carbon pool by folate", "ATIC, DHFR, GART, MTFMT, MTHFD1, MTHFD1L, MTHFS, TYMS", "KEGG", "1.74", "0.17"], ["Cholesterol biosynthesis", "DHCR7, FDFT1, GGPS1, HMGCR, HMGCS1, IDI1, MSMO1, NSDHL, SQLE", "Reactome", "1.77", "0.17"], ["Antigen processing cross presentation", "CD36, CTSS, NCF4, PSMA1, PSMA2, PSMA3, PSMA5, PSMA6, PSMA7, PSMB1, PSMB2, PSMB3, PSMC1, PSMC2, PSMC3, PSMC5, PSMD1, PSMD10, PSMD3, PSMD5, RPS27A, SEC61B, SEC61G, TAP1, UBA52", "Reactome", "1.74", "0.18"], ["Alzheimers disease", "NDUFB6, CYCS, NDUFB3, NDUFA8, UQCR11, NDUFC2, ATP5F1, ATP5E, NDUFB5, UQCR10, COX4I1, COX6A1, COX7C, NDUFB10, NDUFB1, CASP8, NDUFV3, NDUFA6, ATP5H, COX7A2, RYR3, NDUFA2, NDUFC1, NDUFS1, NDUFA1, SDHA, NDUFB8, NDUFA4, NDUFA5, APAF1, UQCRH, ATP5O, NDUFA7, NDUFS6, NDUFS4, ATP5D, ATP5C1, NDUFB9, CACNA1D, NDUFS8, NDUFS3, NDUFS7, CASP3, COX8A, COX6C, COX5A, NDUFA10, ATP2A1, COX7A2L, TNFRSF1A, UQCRFS1, PSEN1, NDUFB4, IL1B, PLCB1, NCSTN, PLCB4", "KEGG", "1.74", "0.19"], ["Parkinsons disease", "APAF1, ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5H, ATP5O, CASP3, COX4I1, COX5A, COX6A1, COX6C, COX7A2, COX7A2L, COX7C, COX8A, CYCS, GPR37, NDUFA1, NDUFA10, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, PARK7, PPID, SDHA, SLC25A4, SNCAIP, UBE2L3, UQCR10, UQCR11, UQCRH, VDAC3", "KEGG", "1.77", "0.19"], ["TCA cycle and respiratory electron transport", "ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5H, ATP5I, ATP5J2, ATP5O, COX4I1, COX5A, COX6A1, COX6C, COX7A2L, COX7C, COX8A, CYCS, D2HGDH, DLD, IDH3A, LDHB, NDUFA1, NDUFA10, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, NNT, SDHA, SUCLG1, SUCLG2, UQCR11, UQCRH", "Reactome", "1.72", "0.19"], ["Respiratory electron transport", "COX4I1, COX5A, COX6A1, COX6C, COX7A2L, COX7C, COX8A, CYCS, NDUFA1, NDUFA10, NDUFA12, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB4, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, SDHA, UQCR11, UQCRFS1, UQCRH", "Reactome", "1.81", "0.21"], ["Respiratory electron transport ATP synthesis by chemiosmotic coupling and heat production by uncoupling proteins", "ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5H, ATP5I, ATP5J2, ATP5O, COX4I1, COX5A, COX6A1, COX6C, COX7A2L, COX7C, COX8A, CYCS, NDUFA1, NDUFA10, NDUFA12, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB4, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, SDHA, UCP3, UQCR11, UQCRFS1, UQCRH", "Reactome", "1.83", "0.23"], ["Translation", "EEF1B2, EIF2B1, EIF2B2, EIF2S1, EIF2S2, EIF2S3, EIF3D, EIF3H, EIF3I, EIF3J, EIF4EBP1, EIF4H, EIF5B, RPL10A, RPL11, RPL13, RPL14, RPL18A, RPL19, RPL21, RPL22, RPL23A, RPL24, RPL26L1, RPL27, RPL27A, RPL29, RPL30, RPL32, RPL35, RPL35A, RPL36, RPL36A, RPL37, RPL37A, RPL38, RPL39, RPL5, RPL6, RPL7, RPL8, RPLP1, RPLP2, RPN1, RPS10, RPS11, RPS14, RPS15, RPS15A, RPS16, RPS2, RPS20, RPS23, RPS24, RPS25, RPS26, RPS27A, RPS28, RPS29, RPS3, RPS3A, RPS4X, RPS6, RPS7, RPS8, RPSA, SEC61B, SEC61G, SPCS1, SPCS2, SPCS3, SRP19, SRP72, SSR3, UBA52", "Reactome", "1.69", "0.24"], ["ER phagosome pathway", "PSMA1, PSMA2, PSMA3, PSMA5, PSMA6, PSMA7, PSMB1, PSMB2, PSMB3, PSMC1, PSMC2, PSMC3, PSMC5, PSMD1, PSMD10, PSMD3, PSMD5, RPS27A, SEC61B, SEC61G, TAP1, UBA52", "Reactome", "1.67", "0.25"]], "row_count": 14, "column_count": 5, "numeric_cells": 37, "header_rows": 1, "locator": "section[15]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:29967729:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:87f9e0f0ffe8ee8f010e2ebe6563b2508b0030532b0c9843907cf09e63674195", "bytes": 3655, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#table-2", "version": null, "note": "Summary statistics for clusters of pathways enriched during FDMI and normal development.Mean Normalised Enrichment Score (NES), false discovery rate (FDR) and signal strength statistic (Signal) for the biological pathways implicated by GSEA in control and FDM. Normal eye development implicated 10 cluster of pathways showing average signal strength while form-deprivation induction implicated 18 clusters of pathways. Pathways shown here only include clustered pathways as represented in Figs. 3 and 4 and do not include pathways that were unclustered. Further detail on the unclustered pathways can be found in File 1. The NES reflects the degree to which a set of genes is overrepresented at either the top or bottom of a ranked list of genes while also taking into account differences in pathway size (i.e., geneset size). NES is the primary statistic for examining enrichment results, and for comparing results across pathways. The percentage signal strength statistic reflects the proportion of the core set of genes that contribute most to a given pathway’s enrichment by accounting for particular genes position in the ranked list. A high signal strength indicates that the genes within a pathway are located close to the top (positive NES) or bottom (negative NES) of the ranked gene list. If the core genes are spread throughout the ranked list, then the signal strength decreases towards zero (Mootha et al., 2003; Subramanian et al., 2005).", "structure": {"pmcid": "PMC6026464", "section_index": 16, "section_title": "Enrichment analysis for long-term FDM induction (FDMI) and recovery (FDMR)", "row_count": 24, "column_count": 9}, "table": {"label": "Table 2", "caption": "Summary statistics for clusters of pathways enriched during FDMI and normal development.Mean Normalised Enrichment Score (NES), false discovery rate (FDR) and signal strength statistic (Signal) for the biological pathways implicated by GSEA in control and FDM. Normal eye development implicated 10 cluster of pathways showing average signal strength while form-deprivation induction implicated 18 clusters of pathways. Pathways shown here only include clustered pathways as represented in Figs. 3 and 4 and do not include pathways that were unclustered. Further detail on the unclustered pathways can be found in File 1. The NES reflects the degree to which a set of genes is overrepresented at either the top or bottom of a ranked list of genes while also taking into account differences in pathway size (i.e., geneset size). NES is the primary statistic for examining enrichment results, and for comparing results across pathways. The percentage signal strength statistic reflects the proportion of the core set of genes that contribute most to a given pathway’s enrichment by accounting for particular genes position in the ranked list. A high signal strength indicates that the genes within a pathway are located close to the top (positive NES) or bottom (negative NES) of the ranked gene list. If the core genes are spread throughout the ranked list, then the signal strength decreases towards zero (Mootha et al., 2003; Subramanian et al., 2005).", "rows": [["Cluster", "Control", "FDMI"], ["", "Pathways in cluster", "NES", "FDR q-value", "Signal", "Pathways in cluster", "NES", "FDR q-value", "Signal"], ["Cell cycle, mitotic", "5", "−2.233", "0.019", "31%", "3", "−2.253", "0.009", "98%"], ["Cell maintenance & survival", "–", "–", "–", "–", "28", "−2.180", "0.014", "117%"], ["Clatherin-mediated endocytosis (CME)", "–", "–", "–", "–", "2", "−2.014", "0.032", "81%"], ["Complement and coagulation cascades (CCC)", "–", "–", "–", "–", "2", "2.708", "0.003", "140%"], ["Cytochrome p450", "2", "2.247", "0.025", "47%", "5", "2.629", "0.002", "133%"], ["Cytokine pathways", "2", "2.717", "0.002", "40%", "–", "–", "–", "–"], ["Neuron structure/growth", "–", "–", "–", "–", "5", "−2.321", "0.007", "80%"], ["Fatty acid (FA) metabolism", "–", "–", "–", "–", "2", "−1.886", "0.032", "84%"], ["Glucosaminoglycan (GAG) metabolism", "4", "2.121", "0.029", "40%", "–", "–", "–", "–"], ["Ion channel transport", "–", "–", "–", "–", "2", "−2.331", "0.007", "99%"], ["Mitochondrial energy metabolism", "–", "–", "–", "–", "7", "2.396", "0.005", "47%"], ["Neurotransmission", "5", "−2.522", "0.011", "37%", "8", "−2.423", "0.007", "103%"], ["Peroxisome", "2", "−2.221", "0.017", "40%", "–", "–", "–", "–"], ["Phospholipid metabolism", "2", "−2.134", "0.026", "28%", "3", "−1.939", "0.027", "57%"], ["Signal transduction, growth factors (GF)", "–", "–", "–", "–", "4", "−1.984", "0.021", "66%"], ["Signal transduction, g-protein coupled receptors (GPCR)", "7", "2.572", "0.019", "52%", "7", "2.683", "0.010", "122%"], ["Signal transduction, mitogen-activated protein kinases (MAPK)", "–", "–", "–", "–", "4", "−1.931", "0.028", "67%"], ["Signal transduction, nerve growth factor (NGF)", "–", "–", "–", "–", "5", "−2.195", "0.014", "84%"], ["Transcription", "–", "–", "–", "–", "10", "−2.218", "0.013", "120%"], ["Translation", "–", "–", "–", "–", "8", "2.731", "0.001", "46%"], ["Ubiquitin-mediated proteolysis", "3", "−2.491", "0.006", "39%", "–", "–", "–", "–"], ["Vesicle-mediated transport", "3", "−2.152", "0.025", "40%", "3", "−2.097", "0.013", "103%"]], "row_count": 24, "column_count": 9, "numeric_cells": 113, "header_rows": 2, "locator": "section[16]/table-wrap[1]#table-2"}}], "gaps": ["asset:data:geo:GSE6543 not downloaded", "asset:data:geo:GSE6543 licence not read", "asset:data:geo:GSE89325 not downloaded", "asset:data:geo:GSE89325 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Gene Set Enrichment Analysis (GSEA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "“The Broad Institute’s Gene Set Enrichment Analysis (GSEA) software was used to determine whether a priori defined sets of genes were significantly enriched (Mootha et al., 2003; Subramanian et al., 2005) during the induction and recovery of FD.”"}}], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Gene Set Enrichment Analysis (GSEA)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE6543", "GSE89325"], "resolved_accessions": ["GSE6543", "GSE89325"], "statements": ["The following information was supplied regarding data availability:The data discussed in this article are available in NCBI’s Gene Expression Omnibus under accession number GSE89325."], "basis": "The paper names GSE6543, GSE89325 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:29967729", "data:geo:GSE6543", "asset:table:pmid:29967729:1", "asset:table:pmid:29967729:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE6543"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:53Z", "independence": "same_provider"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 211746, "completion_tokens": 3323, "cached_tokens": 1840}}, "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:29967729", "type": "paper", "label": "pmid:29967729"}, {"id": "source:pmid:29967729", "type": "manuscript", "label": "PMID 29967729 full text"}, {"id": "data:geo:GSE6543", "type": "dataset", "label": "GEO GSE6543"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29967729", "type": "paper", "label": "pmid:29967729"}, {"id": "source:pmid:29967729", "type": "manuscript", "label": "PMID 29967729 full text"}, {"id": "data:geo:GSE6543", "type": "dataset", "label": "GEO GSE6543"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29967729", "type": "extraction", "used": ["source:pmid:29967729"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE6543", "type": "accession_resolution", "used": ["data:geo:GSE6543"], "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:29967729", "parent_hash": "sha256:0e0584d9d7564be48f4d8ba49c4ea9076cb93f6ecc454ae1ffe3f46af0b75a8a", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE6543 licence not read", "asset:data:geo:GSE6543 not downloaded", "asset:data:geo:GSE89325 licence not read", "asset:data:geo:GSE89325 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": ["PURPOSE: RNA sequencing analysis has demonstrated bidirectional chan", "E model of myopia. METHODS: Archived genomic transcriptome data from the first three days of induction"], "order_basis": "paper_text_order:190", "id": "assay:1"}, {"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": ["ing report for myopia induction and recovery microarray studiesForm-deprivation (FD) myopia inductio"], "order_basis": "paper_text_order:6020", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:13:33+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}}}