{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30666314", "kind": "science-record", "revision": 8, "content_hash": "sha256:21d3fc44139195cf654532aca79ce7732e6235395567a77cfc5e03fcd2276f21", "created_at": "2026-11-01T15:40:41Z", "updated_at": "2026-11-01T22:43:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated dataset on acute phase protein response in chicken challenged with Escherichia coli lipopolysaccharide endotoxin.", "doi": "10.1016/j.dib.2018.09.103", "pmid": "30666314", "authors": ["Anita Horvatić", "Nicolas Guillemin", "Haider Kaab", "Dorothy McKeegan", "Emily O'Reilly", "Maureen Bain", "Josipa Kuleš", "Peter David Eckersall"], "journal": "Data in brief", "year": 2018, "abstract": "Data herein describe the quantitative changes in the plasma proteome in chickens challenged with lipopolysaccharide (LPS), a bacterial endotoxin known to stimulate the host innate immune system obtained by shotgun quantitative proteomic tandem mass tags approach using high-resolution Orbitrap technology. Statistical and bioinformatic analyses were performed to specify the effect of bacterial endotoxin. Plasma from chicken (N=6) challenged with Escherichia coli (LPS) (2 mg/kg body weight) was collected pre (0 h) and at 12, 24, 48, and 72 h post injection along with plasma from a control group (N=6) challenged with sterile saline. Protein identification and relative quantification were performed using Proteome Discoverer, and data were analysed using R. Gene Ontology terms were analysed by the Cytoscape application ClueGO based on Gallus gallus GO Biological Process database, and refined by REVIGO. Absolute quantification of several acute phase proteins, e.g. alpha-1-acid glycoprotein (AGP), serum amyloid A (SAA) and ovotrensferrin (OVT) was performed by immunoassays to validate the LC-MS results. The data contained within this article are directly related to our research article\"Quantitative proteomics using tandem mass tags in relation to the acute phase protein response in chicken challenged with Escherichia coli lipopolysaccharide endotoxin\" [1]. The raw mass spectrometric data generated in this study were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009399 (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009399).", "claims": [{"id": "claim-method", "statement": "A two-way ANOVA was performed to model the effect of treatment and time on the quantity of the peptides, using a linear regression model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30666314", "locator": "sections[7] \"Statistics for proteomics\" paragraph 3", "quote": "A two-way ANOVA was performed to model the effect of treatment and time on the quantity of the peptides, using a linear regression model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009399MS (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009399). All other data are available within this article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30666314", "locator": "sections[1] \"p\" paragraph 1", "quote": "The mass spectrometry proteomics raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009399MS (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009399). All other data are available within this article."}], "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:30666314"], "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:PXD009399"], "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:PXD009399"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30666314", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2018.09.103", "sha256": "sha256:a52af8cbc016c62d7b3cb3c8709ada903ed3799797a595bbc3b7d012d7411e7f", "bytes": 32215, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2018.09.103", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6205363", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD009399", "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=PXD009399", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD009399", "version": null, "note": "The mass spectrometry proteomics raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009399MS (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009399). All other data are available within this article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009399MS (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009399). All other data are available within this article.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "TMT-based quantitative proteomics of plasma from chicken challenged with lipopolysaccharide endotoxin", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30666314:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:41734d32467839feb890c6d79bdcef932ac2b4715a20f953cf16a19845dada70", "bytes": 1320, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0035", "version": null, "note": null, "structure": {"pmcid": "PMC6205363", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Veterinary medicine, Biomedicine"], ["More specific subject area", "Proteomics, statistics, bioinformatics, immunoassays"], ["Type of data", "Excel files, graphs, figures"], ["How data was acquired", "1.LC-MS/MS analysis was performed using Ultimate 3000 RSLCnano system (Dionex, Germering, Germany) coupled to Q Exactive Plus mass spectrometer (Thermo Fisher Scientific, Bremen, Germany).2.Acute phase proteins absolute quantification was performed using ELISA tests (for AGP, SAA) and radial immunodiffusion (for OVT)."], ["Data format", "Integration of raw and analyzed data"], ["Experimental factors", "Non-depleted plasma samples"], ["Experimental features", "Quantitative proteomic, bioinformatic and immunoassay analyses of chicken serum"], ["Data source location", "University of Glasgow Cochno Farm & Research Centre, Glasgow, United Kingdom"], ["Data accessibility", "The mass spectrometry proteomics raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009399MS (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009399). 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All other data are available within this article."]], "row_count": 9, "column_count": 2, "numeric_cells": 2, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0035"}}, {"id": "asset:table:pmid:30666314:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d17bf17bec06aeb1f0d99bdd50a151d8c2a745702a43ac0bee82d2c4ffddfbbc", "bytes": 6004, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#t0005", "version": null, "note": "Proteins with significantly differential abundances between LPS and saline groups identified using TMT approach.", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 89, "column_count": 4}, "table": {"label": "Table 1", "caption": "Proteins with significantly differential abundances between LPS and saline groups identified using TMT approach.", "rows": [["Gene Symbol"], ["(Gallus gallus)", "Protein name", "P-value (FDR)", "Fold Change"], ["HPS5", "serum amyloid A protein", "2.20E-03", "1.24"], ["SERPINA3", "alpha-1-antiproteinase*", "7.89E-07", "1.02"], ["HPX", "haemopexin*", "5.35E-06", "0.79"], ["ORM1", "alpha 1-acid glycoprotein", "1.05E-05", "0.66"], ["LCN8", "extracellular fatty acid-binding protein precursor", "7.62E-03", "0.65"], ["TF", "ovotransferrin", "3.61E-06", "0.49"], ["CP", "ceruloplasmin*", "1.14E-03", "0.48"], ["SMC4", "condensin complex subunit", "1.94E-03", "0.47"], ["LOC107051143", "complement C3-like*", "2.09E-05", "0.43"], ["CFD", "complement factor D, partial*", "1.05E-04", "0.34"], ["LOC423629", "uncharacterized protein LOC423629*", "1.87E-03", "0.33"], ["LOC419851", "complement regulatory soluble protein", "9.47E-03", "0.32"], ["PIT54", "PIT 54", "1.17E-04", "0.29"], ["LOC100858647", "beta-microseminoprotein-like*", "2.99E-03", "0.28"], ["FGA", "Fibrinogen alpha chain precursor", "4.45E-05", "0.26"], ["CLU", "clusterin isoform X1*", "6.86E-03", "0.21"], ["FGB", "Fibrinogen beta chain precursor", "2.46E-04", "0.21"], ["FGG", "fibrinogen gamma chain precursor", "1.10E-04", "0.21"], ["C3", "complement C3 precursor", "1.41E-03", "0.19"], ["IGLL1", "immunoglobulin light chain variable region, partial", "1.79E-02", "0.18"], ["CFHR2", "complement factor H*", "1.64E-05", "0.17"], ["SPINK5", "ovoinhibitor", "2.87E-02", "0.17"], ["A2ML4", "alpha-2-macroglobulin-like protein 1*", "8.86E-03", "0.17"], ["VNN1", "pantetheinase precursor", "3.69E-02", "0.17"], ["APOH", "beta-2-glycoprotein 1 precursor", "3.50E-03", "0.15"], ["FETUB", "fetuin-B precursor", "8.55E-06", "0.15"], ["PLG", "plasminogen*", "3.20E-06", "0.12"], ["ATRN", "attractin isoform X3*", "3.08E-02", "0.11"], ["LOC418892", "uncharacterized protein", "2.78E-02", "0.11"], ["CST3", "cystatin precursor", "2.25E-02", "−0.10"], ["TNC", "tenascin", "4.09E-02", "−0.11"], ["ITIH3", "inter-alpha-trypsin inhibitor heavy chain H3 isoform X1*", "4.21E-02", "−0.12"], ["AGRN", "basement membrane-specific heparan sulfate proteoglycan core protein precursor", "2.51E-02", "−0.12"], ["ITIH2", "inter-alpha-trypsin inhibitor heavy chain H2 precursor", "1.96E-02", "−0.12"], ["IGFALS", "insulin-like growth factor-binding protein complex acid labile subunit isoform X1*", "3.71E-03", "−0.13"], ["HSPG2", "basement membrane-specific heparan sulfate proteoglycan core protein*", "1.79E-02", "−0.13"], ["HRG", "histidine-rich glycoprotein*", "1.51E-02", "−0.14"], ["COL5A1", "alpha 1 (V) collagen", "2.79E-02", "−0.14"], ["KNG1", "kininogen-1*", "1.19E-03", "−0.14"], ["C1QTNF3", "complement C1q tumor necrosis factor-related protein 3 isoform X1*", "8.85E-03", "−0.14"], ["F13A1", "coagulation factor XIII A chain", "4.15E-02", "−0.14"], ["LUM", "lumican precursor", "2.45E-03", "−0.14"], ["AHSG", "alpha-2-HS-glycoprotein*", "3.98E-02", "−0.14"], ["GIF", "hypothetical protein RCJMB04_7i4", "3.80E-02", "−0.15"], ["PROS1", "vitamin K-dependent protein S*", "1.42E-02", "−0.15"], ["APOA2", "apolipoprotein A-II*", "2.47E-02", "−0.16"], ["ANPEP", "aminopeptidase, partial", "2.11E-02", "−0.16"], ["LOC107056848", "cadherin-5-like, partial*", "7.56E-03", "-0.17"], ["VTN", "vitronectin precursor", "1.59E-05", "−0.17"], ["CL2", "ribonuclease CL2 precursor", "1.69E-02", "−0.17"], ["LOC107055759", "vitamin K-dependent protein S-like*", "7.86E-03", "−0.17"], ["APOA1", "apolipoprotein A-I", "1.64E-05", "−0.18"], ["FBLN1", "fibulin-1, isoform D precursor", "3.85E-02", "−0.18"], ["APOA4", "apolipoprotein A-IV precursor", "4.10E-04", "−0.19"], ["IL6ST", "interleukin-6 receptor subunit beta precursor", "4.32E-05", "−0.20"], ["TFRC", "chicken transferrin receptor", "2.19E-04", "−0.20"], ["SPARC", "basement-membrane protein 40 precursor", "3.29E-02", "−0.20"], ["F13B", "coagulation factor XIII B chain isoform X1*", "9.61E-03", "−0.20"], ["LOC100857892", "sushi, nidogen and EGF-like domain-containing protein 1 isoform X1*", "8.56E-03", "−0.20"], ["LOC107050076", "IgGFc-binding protein-like, partial*", "4.78E-03", "−0.21"], ["SERPINF1", "pigment epithelium-derived factor precursor", "3.03E-06", "−0.21"], ["CLEC3B", "tetranectin precursor", "7.32E-03", "−0.22"], ["SERPINC1", "antithrombin-III*", "1.39E-06", "−0.23"], ["SERPINA4", "serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4 precursor", "3.23E-04", "−0.23"], ["LOC771012", "coagulation factor X-like*", "4.19E-03", "−0.23"], ["ENO1", "alpha-enolase", "6.46E-03", "−0.23"], ["LOC100858068", "IgGFc-binding protein-like, partial*", "2.32E-02", "−0.23"], ["RBP4A", "E Chain E, Retinol Binding Protein Complexed With Transthyretin", "2.26E-04", "-0.25"], ["FN1", "fibronectin, partial", "9.44E-03", "−0.26"], ["SERPINA5", "alpha-1-antitrypsin isoform X1*", "2.49E-04", "−0.28"], ["TGFBI", "transforming growth factor-beta-induced protein ig-h3 precursor", "3.84E-06", "−0.28"], ["HBG2", "beta-globin", "1.46E-02", "−0.29"], ["LCAT", "lecithin-cholesterol acyltransferase, partial", "1.14E-02", "−0.29"], ["C4", "complement C4 precursor", "3.37E-02", "−0.30"], ["ALPP", "intestinal-type alkaline phosphatase*", "1.27E-02", "−0.30"], ["POSTN", "periostin precursor", "3.16E-06", "−0.32"], ["COL1A1", "collagen alpha-1(I) chain*", "2.52E-05", "−0.36"], ["SCARA5", "scavenger receptor class A member 5 isoform X1*", "1.97E-02", "−0.36"], ["LOC776376", "pentraxin-related precursor", "1.82E-02", "−0.39"], ["HBAD", "alpha-D globin", "3.10E-02", "−0.43"], ["COL6A1", "collagen alpha-1(VI) chain precursor", "2.07E-06", "−0.44"], ["CPN2", "carboxypeptidase N subunit 2*", "2.11E-05", "−0.46"], ["LRRC15", "uncharacterized protein LRRC15*", "2.11E-05", "−0.46"], ["HBAA", "hemoglobin subunit alpha-A chain", "7.37E-03", "−0.48"], ["KRT8", "keratin, type II cytoskeletal 8*", "3.35E-02", "−0.50"], ["LOC107055417", "keratin, type II cytoskeletal 8-like, partial*", "3.35E-02", "−0.50"], ["COL1A2", "collagen alpha-2(I) chain precursor", "7.52E-04", "−0.51"]], "row_count": 89, "column_count": 4, "numeric_cells": 217, "header_rows": 2, "locator": "section[3]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:30666314:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:27a693fb0f7a37ab02b14c744f6814b0d242fc32dfc2e11f19801deee308f388", "bytes": 1393, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#t0010", "version": null, "note": "Proteins with significantly differential abundances during time in chicken challenged with Escherichia coli lipopolysaccharide endotoxin.", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 20, "column_count": 6}, "table": {"label": "Table 2", "caption": "Proteins with significantly differential abundances during time in chicken challenged with Escherichia coli lipopolysaccharide endotoxin.", "rows": [["Gene symbol", "P value (FDR)", "Fold change (12 h/0 h)", "Fold change (24 h/0 h)", "Fold change (48 h/0 h)", "Fold change (72 h/0 h)"], ["A2ML4", "1.57E-02", "0.34", "0.44", "0.31", "0.19"], ["AHSG", "1.06E-02", "−0.43", "−0.15", "−0.04", "0.13"], ["APOA2", "1.37E-02", "−0.36", "−0.49", "−0.19", "−0.30"], ["C3", "4.39E-02", "0.18", "0.35", "0.35", "0.19"], ["CFD", "1.89E-02", "0.42", "0.61", "0.62", "0.43"], ["COL1A1", "3.39E-02", "−0.62", "−0.42", "−0.42", "−0.23"], ["CP", "3.16E-03", "1.02", "1.05", "0.51", "0.21"], ["FGA", "9.93E-03", "0.29", "0.38", "0.23", "0.03"], ["FGB", "1.03E-02", "0.26", "0.34", "0.24", "0.03"], ["FGG", "9.19E-03", "0.23", "0.33", "0.23", "0.01"], ["HPS5", "5.44E-03", "2.27", "1.35", "0.35", "-0.29"], ["HPX", "7.81E-03", "0.76", "1.20", "1.21", "0.94"], ["ITIH2", "4.46E-02", "−0.19", "−0.05", "0.02", "0.04"], ["LCN8", "1.82E-02", "1.78", "1.02", "0.66", "0.21"], ["ORM1", "5.01E-03", "0.93", "1.18", "0.76", "0.42"], ["POSTN", "2.18E-02", "0.06", "−0.30", "−0.35", "−0.15"], ["SERPINA3", "4.31E-03", "1.24", "1.35", "0.99", "0.73"], ["TF", "1.54E-02", "0.51", "0.55", "0.41", "0.30"], ["TGFBI", "1.50E-02", "−0.34", "−0.52", "−0.29", "−0.24"]], "row_count": 20, "column_count": 6, "numeric_cells": 99, "header_rows": 1, "locator": "section[3]/table-wrap[2]#t0010"}}, {"id": "asset:table:pmid:30666314:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:33c68b7dabced4c3e85eefcfe32a7387849d3154bbf06592c5445033c3e91062", "bytes": 2765, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[3]#t0015", "version": null, "note": "GO terms over-represented in chicken challenged with Escherichia coli lipopolysaccharide endotoxin vs saline group.", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 26, "column_count": 8}, "table": {"label": "Table 3", "caption": "GO terms over-represented in chicken challenged with Escherichia coli lipopolysaccharide endotoxin vs saline group.", "rows": [["GOID", "GOTerm", "Term p-value", "Genes", "Cluster", "Redundant", "Leader", "Group"], ["GO:0072378", "blood coagulation, fibrin clot formation", "1.18E-12", "6", "No specific", "", "", "GO:0052547"], ["GO:0031589", "cell-substrate adhesion", "1.76E-04", "7", "No specific", "", "Yes", "GO:0031589"], ["GO:0015893", "drug transport", "6.75E-03", "4", "Negative", "", "", "GO:1902042"], ["GO:0035987", "endodermal cell differentiation", "5.95E-04", "3", "Negative", "", "", "GO:0052547"], ["GO:0030198", "extracellular matrix organization", "6.46E-03", "4", "Negative", "", "", "GO:0043062"], ["GO:0043062", "extracellular structure organization", "8.25E-04", "6", "Negative", "", "Yes", "GO:0043062"], ["GO:0030195", "negative regulation of blood coagulation", "1.75E-06", "5", "Positive", "Yes", "", "NA"], ["GO:0010951", "negative regulation of endopeptidase activity", "9.55E-18", "16", "Negative", "Yes", "", "NA"], ["GO:2000352", "negative regulation of endothelial cell apoptotic process", "4.89E-04", "3", "Positive", "", "", "GO:1902042"], ["GO:1902042", "negative regulation of extrinsic apoptotic signaling pathway via death domain receptors", "4.17E-04", "3", "Positive", "", "Yes", "GO:1902042"], ["GO:0031639", "plasminogen activation", "3.14E-04", "3", "Positive", "", "", "GO:0052547"], ["GO:0070527", "platelet aggregation", "4.19E-03", "3", "Positive", "Yes", "", "NA"], ["GO:0022409", "positive regulation of cell-cell adhesion", "3.36E-03", "4", "Positive", "", "", "GO:0031589"], ["GO:0045921", "positive regulation of exocytosis", "4.19E-03", "3", "Positive", "Yes", "", "NA"], ["GO:0090277", "positive regulation of peptide hormone secretion", "4.94E-04", "4", "Positive", "", "", "GO:1902042"], ["GO:0050714", "positive regulation of protein secretion", "4.76E-03", "4", "Positive", "Yes", "", "NA"], ["GO:0045907", "positive regulation of vasoconstriction", "6.99E-04", "3", "Positive", "", "", "GO:0052547"], ["GO:0072376", "protein activation cascade", "2.79E-13", "9", "No specific", "", "", "GO:0052547"], ["GO:0016485", "protein processing", "1.58E-03", "5", "Positive", "Yes", "", "NA"], ["GO:0030193", "regulation of blood coagulation", "6.70E-08", "7", "No specific", "Yes", "", "NA"], ["GO:0010810", "regulation of cell-substrate adhesion", "9.15E-03", "3", "Negative", "Yes", "", "NA"], ["GO:0051336", "regulation of hydrolase activity", "1.52E-10", "20", "Negative", "", "", "GO:0052547"], ["GO:0052547", "regulation of peptidase activity", "1.62E-17", "18", "Negative", "", "Yes", "GO:0052547"], ["GO:0051592", "response to calcium ion", "4.15E-03", "3", "Positive", "", "", "GO:1902042"], ["GO:0042060", "wound healing", "7.79E-07", "10", "Negative", "Yes", "", "NA"]], "row_count": 26, "column_count": 8, "numeric_cells": 91, "header_rows": 1, "locator": "section[3]/table-wrap[3]#t0015"}}, {"id": "asset:table:pmid:30666314:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:366a827b0bee3f1202f60bd97113c832b90c07c2cde56b68358a6d97aff71d8f", "bytes": 1600, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[4]#t0020", "version": null, "note": "GO terms over-represented in chicken challenged with Escherichia coli lipopolysaccharide endotoxin during time.", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 15, "column_count": 7}, "table": {"label": "Table 4", "caption": "GO terms over-represented in chicken challenged with Escherichia coli lipopolysaccharide endotoxin during time.", "rows": [["GOID", "GOTerm", "Term p-value", "Genes", "Redundant", "Leader", "Group"], ["GO:0006953", "acute-phase response", "7.12E-06", "3", "", "", "GO:0072376"], ["GO:0010951", "negative regulation of endopeptidase activity", "3.40E-05", "4", "", "", "GO:0072376"], ["GO:0072376", "protein activation cascade", "6.11E-07", "4", "", "Yes", "GO:0072376"], ["GO:0034116", "positive regulation of heterotypic cell-cell adhesion", "4.60E-07", "3", "", "Yes", "GO:0034116"], ["GO:0051592", "response to calcium ion", "5.96E-05", "3", "", "", "GO:0072376"], ["GO:0070527", "platelet aggregation", "5.32E-05", "3", "Yes", "", "GO:0072376"], ["GO:0045921", "positive regulation of exocytosis", "5.32E-05", "3", "Yes", "", "GO:0072376"], ["GO:0042730", "fibrinolysis", "3.15E-06", "3", "", "", "GO:0072376"], ["GO:0045907", "positive regulation of vasoconstriction", "7.12E-06", "3", "", "", "GO:0072376"], ["GO:0050714", "positive regulation of protein secretion", "1.72E-04", "3", "Yes", "", "GO:0072376"], ["GO:0090277", "positive regulation of peptide hormone secretion", "4.96E-05", "3", "", "", "GO:0072376"], ["GO:0031639", "plasminogen activation", "3.15E-06", "3", "", "", "GO:0072376"], ["GO:1902042", "negative regulation of extrinsic apoptotic signaling pathway via death domain receptors", "3.99E-06", "3", "", "", "GO:0072376"], ["GO:2000352", "negative regulation of endothelial cell apoptotic process", "4.80E-06", "3", "", "", "GO:0072376"]], "row_count": 15, "column_count": 7, "numeric_cells": 56, "header_rows": 1, "locator": "section[3]/table-wrap[4]#t0020"}}, {"id": "asset:table:pmid:30666314:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:071c2db3fd4254bb8ea018386a87357dc7a23fb9f58ebfc7cafd79e7af374509", "bytes": 495, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[5]#t0025", "version": null, "note": "P-values of group and time effects on alpha-1-acid glycoprotein (AGP), serum amyloid A (SAA), and ovotransferrin (OVT) proteins quantified by ELISA.", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 4, "column_count": 5}, "table": {"label": "Table 5", "caption": "P-values of group and time effects on alpha-1-acid glycoprotein (AGP), serum amyloid A (SAA), and ovotransferrin (OVT) proteins quantified by ELISA.", "rows": [["Protein", "Group", "Group x time", "Time - LPS group", "Time – saline group"], ["AGP", "<0.001", "<0.001", "<0.001", "NS"], ["SAA", "<0.001", "<0.001", "<0.001", "NS"], ["OVT", "<0.001", "<0.001", "<0.001", "NS"]], "row_count": 4, "column_count": 5, "numeric_cells": 9, "header_rows": 1, "locator": "section[3]/table-wrap[5]#t0025"}}, {"id": "asset:table:pmid:30666314:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:68d12d24846f6c5d644b9860315e9c4fd4513c32c66b69b157f4e8e6c6668444", "bytes": 1267, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[6]#t0030", "version": null, "note": "Time effect for alpha-1-acid glycoprotein (AGP), serum amyloid A (SAA), and ovotransferrin (OVT) proteins quantified by ELISA. A. Effect of group (LPS versus saline) for each time point, saline used as reference to compare. B. Effect of time on proteins fold change compared with 0 h (reference level).", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 17, "column_count": 7}, "table": {"label": "Table 6", "caption": "Time effect for alpha-1-acid glycoprotein (AGP), serum amyloid A (SAA), and ovotransferrin (OVT) proteins quantified by ELISA. A. Effect of group (LPS versus saline) for each time point, saline used as reference to compare. B. Effect of time on proteins fold change compared with 0 h (reference level).", "rows": [["A. Group effect (LPS versus saline) for each time point"], ["", "", "0 h", "12 h", "24 h", "48 h", "72 h"], ["AGP", "Fold change", "−0.04", "1.29", "1.68", "1.18", "0.96"], ["P value", "NS", "<0.01", "<0.01", "<0.05", "NS"], ["SAA", "Fold change", "0.73", "5.21", "1.90", "1.71", "0.01"], ["P value", "NS", "<0.01", "<0.01", "<0.05", "NS"], ["OVT", "Fold change", "−0.06", "0.78", "1.05", "0.90", "0.62"], ["P value", "NS", "<0.01", "<0.01", "<0.01", "<0.1"], [""], ["B. Time effect in LPS group compared with 0 h"], ["", "", "12 h/0 h", "24 h/0 h", "48 h/0 h", "72 h/0 h", ""], ["AGP", "Fold change", "2.16", "2.11", "1.22", "0.91", ""], ["P value", "<0.01", "<0.01", "<0.05", "NS"], ["SAA", "Fold change", "5.77", "2.58", "0.44", "−1.53", ""], ["P value", "<0.01", "<0.01", "NS", "NS"], ["OVT", "Fold change", "1.06", "1.41", "1.13", "0.92", ""], ["P value", "<0.01", "<0.01", "<0.01", "<0.01"]], "row_count": 17, "column_count": 7, "numeric_cells": 56, "header_rows": 2, "locator": "section[3]/table-wrap[6]#t0030"}}], "gaps": ["asset:data:geo:PXD009399 not downloaded", "asset:data:geo:PXD009399 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": "A two-way ANOVA was performed to model the effect of treatment and time on the quantity of the peptides, using a linear regression model."}}, {"id": "method-2", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.8, "band": "high", "quote": "linear regression"}}], "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": ["PXD009399"], "resolved_accessions": ["PXD009399"], "statements": ["The mass spectrometry proteomics raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009399MS (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009399). All other data are available within this article."], "basis": "The paper names PXD009399 in ProteomeXchange Consortium via the PRIDE partner repository 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:30666314", "data:geo:PXD009399", "asset:table:pmid:30666314:1", "asset:table:pmid:30666314:2", "asset:table:pmid:30666314:3", "asset:table:pmid:30666314:4", "asset:table:pmid:30666314:5", "asset:table:pmid:30666314:6", "asset:table:pmid:30666314:7", "asset:table:pmid:30666314:8"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD009399"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:28Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28447, "completion_tokens": 1241, "cached_tokens": 9480}}, "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:30666314", "type": "paper", "label": "pmid:30666314"}, {"id": "source:pmid:30666314", "type": "manuscript", "label": "PMID 30666314 full text"}, {"id": "data:geo:PXD009399", "type": "dataset", "label": "GEO PXD009399"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30666314", "type": "paper", "label": "pmid:30666314"}, {"id": "source:pmid:30666314", "type": "manuscript", "label": "PMID 30666314 full text"}, {"id": "data:geo:PXD009399", "type": "dataset", "label": "GEO PXD009399"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30666314", "type": "extraction", "used": ["source:pmid:30666314"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD009399", "type": "accession_resolution", "used": ["data:geo:PXD009399"], "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:30666314", "parent_hash": "sha256:70541a06c41c275bdd2c133533a9bb881e6a70292f23dceaf8ecdd77d38a0860", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD009399 licence not read", "asset:data:geo:PXD009399 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["A two-way ANOVA was performed to model the effect of treatment and time on the quantity of the peptides, using a linear regression model."], "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":"2026-11-04T01:47:10+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}}}