Data from quantitative serum proteomic analysis after laparoscopic gastric plication.

{"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. 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["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", 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["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 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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"]}