{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31431912", "kind": "science-record", "revision": 3, "content_hash": "sha256:8304e3c5d5941bfa5200f409379f87c35fa5c1b23e2716961d9e383a37d028ab", "created_at": "2026-11-01T15:40:48Z", "updated_at": "2026-11-01T18:51:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Data from quantitative serum proteomic analysis after laparoscopic gastric plication.", "doi": "10.1016/j.dib.2019.104077", "pmid": "31431912", "authors": ["Parisa Savedoroudi", "Tue Bjerg Bennike", "Kenneth Kastaniegaard", "Mohammad Talebpour", "Alireza Ghassempour", "Allan Stensballe"], "journal": "Data in brief", "year": 2019, "abstract": "Bariatric surgery is an effective treatment for morbid obesity with a sustained weight loss and improvements in metabolic syndrome. We present a label free quantitative shotgun proteomics approach to analyze the serum proteome of obese people who underwent Laparoscopic Gastric Plication (LGP) as a new bariatric surgery. Pre-surgery serum samples of obese individuals were compared with the serum of the same subjects 1-2 months post-surgery (T1) and 4-5 months post-surgery (T2). The data provide a list of 224 quantifiable proteins with at least two unique peptides that were quantifiable in at least 70% of samples. Gene ontology biological processes and molecular functions of differentially regulated proteins between pre- and post-surgery samples were investigated using WebGestalt online tool. In addition, molecular networks of differentially abundant proteins were determined through Ingenuity Pathway Analysis (IPA) software. This report is related to the research article entitled \"Serum proteome changes and accelerated reduction of fat mass after Laparoscopic Gastric Plication in morbidly obese patients\" (Savedoroudi et al. [1]). Proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository through the identifier PXD010528.", "claims": [{"id": "claim-data-access", "statement": "Data are available within this article and from ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD010528.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31431912", "locator": "sections[1] \"table-wrap\" paragraph 1", "quote": "Data are available within this article and from ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD010528."}], "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:31431912"], "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:PXD010528"], "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:PXD010528"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31431912", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2019.104077", "sha256": "sha256:2f8713020c35098c59e01c0cf78308714dafaa8e839a31e88bc81d8d07cf41c8", "bytes": 13203, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2019.104077", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6580113", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD010528", "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=PXD010528", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD010528", "version": null, "note": "Data are available within this article and from ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD010528.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available within this article and from ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD010528.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Data in support of serum proteomics of Laparoscopic Gastric Plication", "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:31431912:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cc241d935767e5a5145305e27a7b674aa5a2f7dd110eea5ed74c77d1f756df4c", "bytes": 7683, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl1", "version": null, "note": "Description of file-names and MaxQuant output in the ProteomeXchange repository PXD010528. MS files were analyzed in MaxQuant. All samples were analyzed in triplicates. Timepoint 1: 1–2 months post-surgery; Timepoint 2: 4–5 months post-surgery.", "structure": {"pmcid": "PMC6580113", "section_index": 3, "section_title": "Data", "row_count": 126, "column_count": 3}, "table": {"label": "Table 1", "caption": "Description of file-names and MaxQuant output in the ProteomeXchange repository PXD010528. MS files were analyzed in MaxQuant. All samples were analyzed in triplicates. Timepoint 1: 1–2 months post-surgery; Timepoint 2: 4–5 months post-surgery.", "rows": [["Raw file", "Sample", "MS system"], ["2bef-1", "2/Before surgery", "Q Exactive HF"], ["2bef-2", "2/Before surgery", "Q Exactive HF"], ["2bef-3", "2/Before surgery", "Q Exactive HF"], ["2aft1-1", "2/After surgery at timepoint 1", "Q Exactive HF"], ["2aft1-2", "2/After surgery at timepoint 1", "Q Exactive HF"], ["2aft1-3", "2/After surgery at timepoint 1", "Q Exactive HF"], ["3bef-1", "3/Before surgery", "Q Exactive HF"], ["3bef-2", "3/Before surgery", "Q Exactive HF"], ["3bef-3", "3/Before surgery", "Q Exactive HF"], ["3aft1-1", "3/After surgery at timepoint 1", "Q Exactive HF"], ["3aft1-2", "3/After surgery at timepoint 1", "Q Exactive HF"], ["3aft1-3_170725101835", "3/After surgery at timepoint 1", "Q Exactive HF"], ["3aft2-1", "3/After surgery at timepoint 2", "Q Exactive HF"], ["3aft2-2", "3/After surgery at timepoint 2", "Q Exactive HF"], ["3aft2-3", "3/After surgery at timepoint 2", "Q Exactive HF"], ["4bef-1", "4/Before surgery", "Q Exactive HF"], ["4bef-2", "4/Before surgery", "Q Exactive HF"], ["4bef-3", "4/Before surgery", "Q Exactive HF"], ["4aft1-1", "4/After surgery at timepoint 1", "Q Exactive HF"], ["4aft1-2", "4/After surgery at timepoint 1", "Q Exactive HF"], ["4aft1-3", "4/After surgery at timepoint 1", "Q Exactive HF"], ["5bef-1", "5/Before surgery", "Q Exactive HF"], ["5bef-2", "5/Before surgery", "Q Exactive HF"], ["5bef-3", "5/Before surgery", "Q Exactive HF"], ["5aft1-1", "5/After surgery at timepoint 1", "Q Exactive HF"], ["5aft1-2", "5/After surgery at timepoint 1", "Q Exactive HF"], ["5aft1-3", "5/After surgery at timepoint 1", "Q Exactive HF"], ["5aft2-1", "5/After surgery at timepoint 2", "Q Exactive HF"], ["5aft2-2", "5/After surgery at timepoint 2", "Q Exactive HF"], ["5aft2-3", "5/After surgery at timepoint 2", "Q Exactive HF"], ["6bef-1", "6/Before surgery", "Q Exactive HF"], ["6bef-2", "6/Before surgery", "Q Exactive HF"], ["6bef-3", "6/Before surgery", "Q Exactive HF"], ["6aft1-1", "6/After surgery at timepoint 1", "Q Exactive HF"], ["6aft1-2", "6/After surgery at timepoint 1", "Q Exactive HF"], ["6aft1-3", "6/After surgery at timepoint 1", "Q Exactive HF"], ["6aft2-1", "6/After surgery at timepoint 2", "Q Exactive HF"], ["6aft2-2", "6/After surgery at timepoint 2", "Q Exactive HF"], ["6aft2-3", "6/After surgery at timepoint 2", "Q Exactive HF"], ["7bef-1", "7/Before surgery", "Q Exactive HF"], ["7bef-2", "7/Before surgery", "Q Exactive HF"], ["7bef-3", "7/Before surgery", "Q Exactive HF"], ["7aft1-1", "7/After surgery at timepoint 1", "Q Exactive HF"], ["7aft1-2", "7/After surgery at timepoint 1", "Q Exactive HF"], ["7aft1-3", "7/After surgery at timepoint 1", "Q Exactive HF"], ["7aft2-1", "7/After surgery at timepoint 2", "Q Exactive HF"], ["7aft2-2", "7/After surgery at timepoint 2", "Q Exactive HF"], ["7aft2-3", "7/After surgery at timepoint 2", "Q Exactive HF"], ["8bef-1", "8/Before surgery", "Q Exactive HF"], ["8bef-2", "8/Before surgery", "Q Exactive HF"], ["8bef-3", "8/Before surgery", "Q Exactive HF"], ["8aft1-1", "8/After surgery at timepoint 1", "Q Exactive HF"], ["8aft1-2", "8/After surgery at timepoint 1", "Q Exactive HF"], ["8aft1-3_170725085836", "8/After surgery at timepoint 1", "Q Exactive HF"], ["8aft2-1", "8/After surgery at timepoint 2", "Q Exactive HF"], ["8aft2-2", "8/After surgery at timepoint 2", "Q Exactive HF"], ["8aft2-3", "8/After surgery at timepoint 2", "Q Exactive HF"], ["9bef-1", "9/Before surgery", "Q Exactive HF"], ["9bef-2", "9/Before surgery", "Q Exactive HF"], ["9bef-3", "9/Before surgery", "Q Exactive HF"], ["9aft1-1", "9/After surgery at timepoint 1", "Q Exactive HF"], ["9aft1-2", "9/After surgery at timepoint 1", "Q Exactive HF"], ["9aft1-3", "9/After surgery at timepoint 1", "Q Exactive HF"], ["10bef-1", "10/Before surgery", "Q Exactive HF"], ["10bef-2", "10/Before surgery", "Q Exactive HF"], ["10bef-3", "10/Before surgery", "Q Exactive HF"], ["10aft1-1", "10/After surgery at timepoint 1", "Q Exactive HF"], ["10aft1-2", "10/After surgery at timepoint 1", "Q Exactive HF"], ["10aft1-3", "10/After surgery at timepoint 1", "Q Exactive HF"], ["10aft2-1", "10/After surgery at timepoint 2", "Q Exactive HF"], ["10aft2-2", "10/After surgery at timepoint 2", "Q Exactive HF"], ["10aft2-3", "10/After surgery at timepoint 2", "Q Exactive HF"], ["11bef-1", "11/Before surgery", "Q Exactive HF"], ["11bef-2", "11/Before surgery", "Q Exactive HF"], ["11bef-3", "11/Before surgery", "Q Exactive HF"], ["11aft1-1", "11/After surgery at timepoint 1", "Q Exactive HF"], ["11aft1-2", "11/After surgery at timepoint 1", "Q Exactive HF"], ["11aft1-3", "11/After surgery at timepoint 1", "Q Exactive HF"], ["11aft2-1", "11/After surgery at timepoint 2", "Q Exactive HF"], ["11aft2-2", "11/After surgery at timepoint 2", "Q Exactive HF"], ["11aft2-3", "11/After surgery at timepoint 2", "Q Exactive HF"], ["12bef-1", "12/Before surgery", "Q Exactive HF"], ["12bef-2", "12/Before surgery", "Q Exactive HF"], ["12bef-3", "12/Before surgery", "Q Exactive HF"], ["12aft1-1", "12/After surgery at timepoint 1", "Q Exactive HF"], ["12aft1-2", "12/After surgery at timepoint 1", "Q Exactive HF"], ["12aft1-3", "12/After surgery at timepoint 1", "Q Exactive HF"], ["14bef-1", "14/Before surgery", "Q Exactive HF"], ["14bef-2", "14/Before surgery", "Q Exactive HF"], ["14bef-3", "14/Before surgery", "Q Exactive HF"], ["14aft1-1", "14/After surgery at timepoint 1", "Q Exactive HF"], ["14aft1-2", "14/After surgery at timepoint 1", "Q Exactive HF"], ["14aft1-3", "14/After surgery at timepoint 1", "Q Exactive HF"], ["14aft2-1", "14/After surgery at timepoint 2", "Q Exactive HF"], ["14aft2-2", "14/After surgery at timepoint 2", "Q Exactive HF"], ["14aft2-3", "14/After surgery at timepoint 2", "Q Exactive HF"], ["15bef-1", "15/Before surgery", "Q Exactive HF"], ["15bef-2", "15/Before surgery", "Q Exactive HF"], ["15bef-3", "15/Before surgery", "Q Exactive HF"], ["15aft1-1", "15/After surgery at timepoint 1", "Q Exactive HF"], ["15aft1-2", "15/After surgery at timepoint 1", "Q Exactive HF"], ["15aft1-3", "15/After surgery at timepoint 1", "Q Exactive HF"], ["17bef-1", "17/Before surgery", "Q Exactive HF"], ["17bef-2", "17/Before surgery", "Q Exactive HF"], ["17bef-3", "17/Before surgery", "Q Exactive HF"], ["17aft1-1", "17/After surgery at timepoint 1", "Q Exactive HF"], ["17aft1-2", "17/After surgery at timepoint 1", "Q Exactive HF"], ["17aft1-3", "17/After surgery at timepoint 1", "Q Exactive HF"], ["17aft2-1", "17/After surgery at timepoint 2", "Q Exactive HF"], ["17aft2-2", "17/After surgery at timepoint 2", "Q Exactive HF"], ["17aft2-3", "17/After surgery at timepoint 2", "Q Exactive HF"], ["18bef-1", "18/Before surgery", "Q Exactive HF"], ["18bef-2", "18/Before surgery", "Q Exactive HF"], ["18bef-3", "18/Before surgery", "Q Exactive HF"], ["18aft1-1", "18/After surgery at timepoint 1", "Q Exactive HF"], ["18aft1-2", "18/After surgery at timepoint 1", "Q Exactive HF"], ["18aft1-3", "18/After surgery at timepoint 1", "Q Exactive HF"], ["21bef-1", "21/Before surgery", "Q Exactive HF"], ["21bef-2", "21/Before surgery", "Q Exactive HF"], ["21bef-3", "21/Before surgery", "Q Exactive HF"], ["21aft1-1", "21/After surgery at timepoint 1", "Q Exactive HF"], ["21aft1-2", "21/After surgery at timepoint 1", "Q Exactive HF"], ["21aft1-3", "21/After surgery at timepoint 1", "Q Exactive HF"], ["The MaxQuant output in folder \"txt\" contains a range of files containing important search information. Below file was used for further processing in Perseus post-analysis program and quantitative analysis."], ["proteinGroups.txt", "File containing all proteins with corresponding label free quantitative information"]], "row_count": 126, "column_count": 3, "numeric_cells": 246, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tbl1"}}, {"id": "asset:table:pmid:31431912:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d8490fb03b1668a851826d070c308f322546c3b730843e812dcab39f68c92914", "bytes": 2441, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#tbl2", "version": null, "note": "Enrichment analysis of Gene ontology biological process and molecular function for differentially abundant proteins at T1, using WebGestalt online tool.", "structure": {"pmcid": "PMC6580113", "section_index": 3, "section_title": "Data", "row_count": 23, "column_count": 4}, "table": {"label": "Table 2", "caption": "Enrichment analysis of Gene ontology biological process and molecular function for differentially abundant proteins at T1, using WebGestalt online tool.", "rows": [["Gen set", "Description", "P-value", "Overlap Gen-ID"], ["Biological Process"], ["GO:0051223", "regulation of protein transport", "4.87E-05", "CRP, GPLD1, APOA1, APOA2, APOD, IL1RAP, LCP1, SRGN, RBP4, SAA1, CD14, ADIPOQ"], ["GO:0070201", "regulation of establishment of protein localization", "8.84E-05", "CRP, GPLD1, APOA1, APOA2, APOD, IL1RAP, LCP1, SRGN, RBP4, SAA1, CD14, ADIPOQ"], ["GO:0034284", "response to monosaccharide", "0.000109", "GPLD1, APOA2, SERPINF1, APOM, SPARC, THBS1, ADIPOQ"], ["GO:0032880", "regulation of protein localization", "0.000256", "CRP, GPLD1, APOA1, APOA2, APOD, IL1RAP, LCP1, SRGN, RBP4, SAA1, CD14, ADIPOQ"], ["GO:0009743", "response to carbohydrate", "0.000315", "GPLD1, APOA2, SERPINF1, APOM, SPARC, THBS1, ADIPOQ"], ["GO:0009746", "response to hexose", "0.000532", "GPLD1, APOA2, SERPINF1, APOM, THBS1, ADIPOQ"], ["GO:0009749", "response to glucose", "0.000532", "GPLD1, APOA2, SERPINF1, APOM, THBS1, ADIPOQ"], ["GO:0050707", "regulation of cytokine secretion", "0.000746", "CRP, APOA1, APOA2, IL1RAP, SRGN, SAA1, CD14"], ["GO:0051224", "negative regulation of protein transport", "0.00081", "APOA1, APOA2, APOD, SRGN, ADIPOQ"], ["GO:1904950", "negative regulation of establishment of protein localization", "0.00081", "APOA1, APOA2, APOD, SRGN, ADIPOQ"], ["Molecular Function"], ["GO:0005319", "lipid transporter activity", "0.00279", "APOF, APOA1, APOA2, APOD, APOM, RBP4"], ["GO:0005496", "steroid binding", "0.00279", "GC, APOF, APOA1, APOA2, APOD, SHBG"], ["GO:0071813", "lipoprotein particle binding", "0.0101", "CRP, APOA1, APOA2, THBS1"], ["GO:0071814", "protein-lipid complex binding", "0.0101", "CRP, APOA1, APOA2, THBS1"], ["GO:0043178", "alcohol binding", "0.0105", "APOF, APOA1, APOA2, APOD, RBP4"], ["GO:0008289", "lipid binding", "0.0122", "F10, GC, APOF, APOA1, APOA2, APOD, APOM, RBP4, SHBG, THBS1, CD14"], ["GO:0005215", "transporter activity", "0.0128", "GC, HBB, APOF, APOA1, APOA2, APOD, APOM, RBP4"], ["GO:0022892", "substrate-specific transporter activity", "0.0170", "HBB, APOF, APOA1, APOA2, APOD, APOM, RBP4"], ["GO:0015485", "cholesterol binding", "0.0206", "APOF, APOA1, APOA2, APOD"], ["GO:0032934", "sterol binding", "0.0206", "APOF, APOA1, APOA2, APOD"]], "row_count": 23, "column_count": 4, "numeric_cells": 45, "header_rows": 1, "locator": "section[3]/table-wrap[2]#tbl2"}}, {"id": "asset:table:pmid:31431912:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f679aea00896d9748fe3ef4d83f743bf616d0abfc754d1b4bf99808be0eb0f06", "bytes": 2035, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[3]#tbl3", "version": null, "note": "Enrichment analysis of Gene ontology biological process and molecular function for differentially abundant proteins at T2, using WebGestalt online tool.", "structure": {"pmcid": "PMC6580113", "section_index": 3, "section_title": "Data", "row_count": 23, "column_count": 4}, "table": {"label": "Table 3", "caption": "Enrichment analysis of Gene ontology biological process and molecular function for differentially abundant proteins at T2, using WebGestalt online tool.", "rows": [["Gen set", "Description", "P-value", "Overlap Gen-ID"], ["Biological Process"], ["GO:0010976", "positive regulation of neuron projection development", "0.000151", "FN1, IL1RAP, NRP1"], ["GO:0045666", "positive regulation of neuron differentiation", "0.000151", "FN1, IL1RAP, NRP1"], ["GO:0050769", "positive regulation of neurogenesis", "0.000151", "FN1, IL1RAP, NRP1"], ["GO:0051962", "positive regulation of nervous system development", "0.000151", "FN1, IL1RAP, NRP1"], ["GO:0010975", "regulation of neuron projection development", "0.000262", "FN1, IL1RAP, NRP1"], ["GO:0031346", "positive regulation of cell projection organization", "0.000416", "FN1, IL1RAP, NRP1"], ["GO:0045664", "regulation of neuron differentiation", "0.000416", "FN1, IL1RAP, NRP1"], ["GO:0050767", "regulation of neurogenesis", "0.000618", "FN1, IL1RAP, NRP1"], ["GO:0051960", "regulation of nervous system development", "0.000618", "FN1, IL1RAP, NRP1"], ["GO:0031344", "regulation of cell projection organization", "0.00119", "FN1, IL1RAP, NRP1"], ["Molecular Function"], ["GO:0004888", "transmembrane signaling receptor activity", "0.0226", "IL1RAP, NRP1"], ["GO:0099600", "transmembrane receptor activity", "0.0226", "IL1RAP, NRP1"], ["GO:0004872", "receptor activity", "0.0304", "PRG4, IL1RAP, NRP1"], ["GO:0060089", "molecular transducer activity", "0.0304", "PRG4, IL1RAP, NRP1"], ["GO:0038023", "signaling receptor activity", "0.0336", "IL1RAP, NRP1"], ["GO:0004871", "signal transducer activity", "0.0533", "IL1RAP, NRP1"], ["GO:0016301", "kinase activity", "0.135", "NRP1"], ["GO:0016504", "peptidase activator activity", "0.135", "FN1"], ["GO:0016772", "transferase activity, transferring phosphorus-containing groups", "0.135", "NRP1"], ["GO:0016773", "phosphotransferase activity, alcohol group as acceptor", "0.135", "NRP1"]], "row_count": 23, "column_count": 4, "numeric_cells": 40, "header_rows": 1, "locator": "section[3]/table-wrap[3]#tbl3"}}, {"id": "asset:table:pmid:31431912:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5de4dcff6f96ebd5170db54c3c23b862f322f16286c4eb8264abfda57ce3d8e2", "bytes": 2768, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[4]#tbl4", "version": null, "note": "Networks identified using IPA.", "structure": {"pmcid": "PMC6580113", "section_index": 3, "section_title": "Data", "row_count": 9, "column_count": 4}, "table": {"label": "Table 4", "caption": "Networks identified using IPA.", "rows": [["Top Diseases and Functions", "Score", "Focus Molecules", "Molecules in Network"], ["T1"], ["Lipid Metabolism, Molecular Transport, Small Molecule Biochemistry", "45", "19", "Adipokine, ADIPOQ, APCS, APOA1, APOA2, APOA4, APOD, APOF, APOM, C1q, C4BP, C4BPA, Collagen type II, CRP, ERK1/2, F10, Fibrinogen, GC, GPLD1, Growth hormone, HDL, HDL-cholesterol, Histone h4, IL12 (complex), LDL, NADPH oxidase, Pro-inflammatory Cytokine, RARRES2, Rbp, RBP4, SAA1, SERPINF1, SERPINF2, Sod, TTR"], ["Cardiovascular System Development and Function, Cellular Movement, Cell-To-Cell Signaling and Interaction", "28", "13", "Akt, Ap1, collagen, Collagen Alpha1, Collagen type I, Collagen type IV, Collagen type VI, Collagen(s), DBH, DSG2, elastase, Fc gamma receptor, GP1BA, Gp2b3a Receptor, IL1, IL-1R, IL1RAP, Integrin, Iti, ITIH2, ITIH3, Laminin (complex), LCP1, Mek, Mmp, MMP9, p85 (pik3r), Pdgf (complex), PDGF BB, PEPD, SPARC, SRGN, Tgf beta, THBS1, VWF"], ["Cellular Assembly and Organization, Nervous System Development and Function, Cell-To-Cell Signaling and Interaction", "18", "9", "CD14, CFP, Cg, Creb, CRTAC1, ERK, estrogen receptor, F7, FAH, GOT, HBB, HISTONE, Histone h3, Ifn, IFN Beta, Ige, IgG, IgG1, IL12 (family), Immunoglobulin, Insulin, Mapk, NFkB (complex), NRP1, P38 MAPK, PI3K (complex), Pka, PRG4, Rac, RNA polymerase II, SHBG, SRC (family), TCF, Tnf (family), Vegf"], ["Cell-To-Cell Signaling and Interaction, Hematological System Development and Function, Immune Cell Trafficking", "15", "8", "ACTG2, Actin, APCS, APP, C7, CASP8, caspase, CCL17, CD3, CFI, CLEC10A, CNDP1, CTF1, CYTIP, Ddx3x, DEFA6, Dstn/Dstnl1, FETUB, Granzyme, HBG1, IL13, IL10RB, Jnk, LIPA, LRP1, MMRN1, MT1G, PZP, Ras, S100A12, SCAVENGER receptor CLASS A, Sos, SRGN, TCR, ZFP36L1"], ["Inflammatory Response, Infectious Diseases, Inflammatory Disease", "5", "3", "ADIPOR2, APCS, BBS12, CD163, CD276, CLEC10A, CMKLR1, coagulation factor, CYP19, CYTIP, estrone, FBXO42, Fcgr2, FSH, glycosylphosphatidylinositol, GPER1, GPR119, HFE, IL6, IL17B, IL1RL2, LPAR2, N-cor, NfkB1 RelA, PAX8, Proinsulin, RARRES2, S100A12, SCAVENGER receptor CLASS A, SCN9A, SELENOS, SHBG, SMPDL3A, Timp, TNF"], ["T2"], ["Cell-To-Cell Signaling and Interaction, Cell Death and Survival, Inflammatory Response", "21", "7", "Akt, ANGPTL1, B4GALT5, C4BPB, CHST3, CLEC10A, Collagen type VI, CRP, Enolase, ERK, ERK1/2, EXT1, Fc gamma receptor, Fc receptor, FCER1A, FCN1, FN1, GFRA2, HS6ST1, IL1, IL6, IL1RAP, ITIH3, miR-191-5p (and other miRNAs w/seed AACGGAA), NFkB (complex), NfkB1-RelA, NRP1, PRG4, PRSS38, pyridoxamine, S100A12, SEMA3D, SHBG, Stat3-Stat3, TGFB1"]], "row_count": 9, "column_count": 4, "numeric_cells": 18, "header_rows": 1, "locator": "section[3]/table-wrap[4]#tbl4"}}], "gaps": ["asset:data:geo:PXD010528 not downloaded", "asset:data:geo:PXD010528 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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 (not named), 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": ["PXD010528"], "resolved_accessions": ["PXD010528"], "statements": ["Data are available within this article and from ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD010528."], "basis": "The paper names PXD010528 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": [], "assets": ["source:pmid:31431912", "data:geo:PXD010528", "asset:table:pmid:31431912:1", "asset:table:pmid:31431912:2", "asset:table:pmid:31431912:3", "asset:table:pmid:31431912:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD010528"]}, "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": "2026-10-31T18:15:51Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 11620, "completion_tokens": 1100, "cached_tokens": 784}}, "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:31431912", "type": "paper", "label": "pmid:31431912"}, {"id": "source:pmid:31431912", "type": "manuscript", "label": "PMID 31431912 full text"}, {"id": "data:geo:PXD010528", "type": "dataset", "label": "GEO PXD010528"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31431912", "type": "paper", "label": "pmid:31431912"}, {"id": "source:pmid:31431912", "type": "manuscript", "label": "PMID 31431912 full text"}, {"id": "data:geo:PXD010528", "type": "dataset", "label": "GEO PXD010528"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31431912", "type": "extraction", "used": ["source:pmid:31431912"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD010528", "type": "accession_resolution", "used": ["data:geo:PXD010528"], "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:31431912", "parent_hash": "sha256:57f4e7f92be686343dcc431f60ed8707ba216a5bdcc4958785794e5469bab31f", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD010528 licence not read", "asset:data:geo:PXD010528 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"]},"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":"2026-11-04T02:52:30+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}}}