← All .science files
pmid:34445425
Proteomics of Mouse Heart Ventricles Reveals Mitochondria and Metabolism as Major Targets of a Post-Infarction Short-Acting GLP1Ra-Therapy.
Juliana de Freitas Germano · Ankush Sharma · Miroslava Stastna · Chengqun Huang · Marianne Aniag · Angie Aceves · Jennifer E Van Eyk · Robert M Mentzer · Honit Piplani · Allen M Andres · Roberta A Gottlieb
International journal of molecular sciences · 2021 doi:10.3390/ijms22168711
Paper
complete
Experiment
partial
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 11 items
claims array · 1 item
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
data object · 3 fields
assets array · 4 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 65 items
[0] array · 3 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 5 items
[20] array · 5 items
[21] array · 5 items
[22] array · 5 items
[23] array · 5 items
[24] array · 5 items
[25] array · 5 items
[26] array · 5 items
[27] array · 5 items
[28] array · 5 items
[29] array · 5 items
[30] array · 5 items
[31] array · 5 items
[32] array · 5 items
[33] array · 5 items
[34] array · 5 items
[35] array · 5 items
[36] array · 5 items
[37] array · 5 items
[38] array · 5 items
[39] array · 5 items
[40] array · 5 items
[41] array · 5 items
[42] array · 5 items
[43] array · 5 items
[44] array · 5 items
[45] array · 5 items
[46] array · 5 items
[47] array · 5 items
[48] array · 5 items
[49] array · 5 items
[50] array · 5 items
[51] array · 5 items
[52] array · 5 items
[53] array · 5 items
[54] array · 5 items
[55] array · 5 items
[56] array · 5 items
[57] array · 5 items
[58] array · 5 items
[59] array · 5 items
[60] array · 5 items
[61] array · 5 items
[62] array · 5 items
[63] array · 5 items
[64] array · 5 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 3 items
[0] array · 2 items
[1] array · 6 items
[2] array · 6 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 10 items
[0] array · 5 items
[1] array · 5 items
[2] array · 1 item
[3] array · 1 item
[4] array · 5 items
[5] array · 1 item
[6] array · 1 item
[7] array · 5 items
[8] array · 1 item
[9] array · 1 item
gaps array · 0 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 0 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 4 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 5 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[1] object · 11 fields
required_operations array · 3 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34445425", "kind": "science-record", "revision": 7, "content_hash": "sha256:4fc99191e44691dccd461eea386d5fc2499452367ea2df2cf2637a7e1744be70", "created_at": "2026-11-01T15:41:50Z", "updated_at": "2026-11-01T22:04:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomics of Mouse Heart Ventricles Reveals Mitochondria and Metabolism as Major Targets of a Post-Infarction Short-Acting GLP1Ra-Therapy.", "doi": "10.3390/ijms22168711", "pmid": "34445425", "authors": ["Juliana de Freitas Germano", "Ankush Sharma", "Miroslava Stastna", "Chengqun Huang", "Marianne Aniag", "Angie Aceves", "Jennifer E Van Eyk", "Robert M Mentzer", "Honit Piplani", "Allen M Andres", "Roberta A Gottlieb"], "journal": "International journal of molecular sciences", "year": 2021, "abstract": "Cardiovascular disease is the main cause of death worldwide, making it crucial to search for new therapies to mitigate major adverse cardiac events (MACEs) after a cardiac ischemic episode. Drugs in the class of the glucagon-like peptide-1 receptor agonists (GLP1Ra) have demonstrated benefits for heart function and reduced the incidence of MACE in patients with diabetes. Previously, we demonstrated that a short-acting GLP1Ra known as DMB (2-quinoxalinamine, 6,7-dichloro-N-[1,1-dimethylethyl]-3-[methylsulfonyl]-,6,7-dichloro-2-methylsulfonyl-3-N-tert-butylaminoquinoxaline or compound 2, Sigma) also mitigates adverse postinfarction left ventricular remodeling and cardiac dysfunction in lean mice through activation of parkin-mediated mitophagy following infarction. Here, we combined proteomics with in silico analysis to characterize the range of effects of DMB in vivo throughout the course of early postinfarction remodeling. We demonstrate that the mitochondrion is a key target of DMB and mitochondrial respiration, oxidative phosphorylation and metabolic processes such as glycolysis and fatty acid beta-oxidation are the main biological processes being regulated by this compound in the heart. Moreover, the overexpression of proteins with hub properties identified by protein-protein interaction networks, such as Atp2a2, may also be important to the mechanism of action of DMB. Data are available via ProteomeXchange with identifier PXD027867.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD027867 and 10.6019/PXD027867.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34445425", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD027867 and 10.6019/PXD027867."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:34445425"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34445425", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms22168711", "sha256": "sha256:fcb76df63fbd072139d13bf84fa9e02bea2d1b15e6a84d568cc618e67346e630", "bytes": 49633, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms22168711", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8395861", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:34445425:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c2f9330db77425eb574d5143e8aba1a4c5813b8dfc4545d3a923ef8bb08d0f19", "bytes": 4491, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#ijms-22-08711-t001", "version": null, "note": "Unique canonical pathways with predicted z-scores throughout the course of remodeling.", "structure": {"pmcid": "PMC8395861", "section_index": 4, "section_title": "2.2. Oxidative Phosphorylation and Multiple Cellular Metabolic Pathways Are Regulated in the First Week of Post-Infarction Remodeling", "row_count": 65, "column_count": 5}, "table": {"label": "Table 1", "caption": "Unique canonical pathways with predicted z-scores throughout the course of remodeling.", "rows": [["", "Vehicle", "DMB"], ["", "Pathway", "z-Score", "Pathway", "z-Score"], ["Day 1 vs. Naive", "TCA Cycle II (Eukaryotic)", "−2", "Estrogen Receptor Signaling", "1.342"], ["", "NAD signaling pathway", "−1.633", "GP6 Signaling Pathway", "0.447"], ["", "", "", "Production of Nitric Oxide and Reactive Oxygen Species in Macrophages", "0.447"], ["", "", "", "RhoA Signaling", "1.633"], ["", "", "", "RhoGDI Signaling", "−1.000"], ["", "", "", "Signaling by Rho Family GTPases", "2.000"], ["", "", "", "Unfolded protein response", "2.000"], ["", "", "", "Xenobiotic Metabolism AHR Signaling Pathway", "−2.236"], ["", "", "", "Xenobiotic Metabolism CAR Signaling Pathway", "0.378"], ["", "", "", "Xenobiotic Metabolism PXR Signaling Pathway", "−1.633"], ["Day 3 vs. Day 1", "PFKFB4 Signaling Pathway", "−1.000", "Apelin Cardiomyocyte Signaling Pathway", "−0.447"], ["", "RhoA signaling", "2.000", "Aspartate Degradation II", "−2.000"], ["", "Calcium signaling", "0.477", "BAG2 Signaling Pathway", "1.342"], ["", "", "", "Cardiac Hypertrophy Signaling", "−0.447"], ["", "", "", "Cdc42 Signaling", "−1.000"], ["", "", "", "Coagulation System", "0.447"], ["", "", "", "Death Receptor Signaling", "−0.447"], ["", "", "", "ERK/MAPK Signaling", "2.000"], ["", "", "", "Estrogen Receptor Signaling", "−2.309"], ["", "", "", "Gluconeogenesis I", "−2.000"], ["", "", "", "Hepatic Fibrosis Signaling Pathway", "−1.633"], ["", "", "", "HER-2 Signaling in Breast Cancer", "2.000"], ["", "", "", "Insulin Secretion Signaling Pathway", "−0.447"], ["", "", "", "Integrin Signaling", "1.134"], ["", "", "", "NAD Signaling Pathway", "−2.449"], ["", "", "", "Necroptosis Signaling Pathway", "−2.000"], ["", "", "", "Nitric Oxide Signaling in the Cardiovascular System", "1.000"], ["", "", "", "PI3K/AKT Signaling", "1.000"], ["", "", "", "PPARα/RXRα Activation", "−2.236"], ["", "", "", "Production of Nitric Oxide and Reactive Oxygen Species in Macrophages", "1.000"], ["", "", "", "Regulation of Actin-based Motility by Rho", "−1.000"], ["", "", "", "RhoGDI Signaling", "1.342"], ["", "", "", "Role of PKR in Interferon Induction and Antiviral Response", "−1.342"], ["", "", "", "Semaphorin Neuronal Repulsive Signaling Pathway", "−2.236"], ["", "", "", "Senescence Pathway", "−1.633"], ["", "", "", "Signaling by Rho Family GTPases", "−0.447"], ["", "", "", "Superpathway of Methionine Degradation", "−2.236"], ["", "", "", "TCA Cycle II (Eukaryotic)", "−3.317"], ["", "", "", "Unfolded protein response", "1.633"], ["", "", "", "Isoleucine Degradation I", "−2.000"], ["Day 7 vs. Day 3", "Adrenomedullin signaling pathway", "1.000", "14-3-3-mediated Signaling", "2.000"], ["", "Apelin Adipocyte Signaling Pathway", "−2.000", "Acetyl-CoA Biosynthesis I (Pyruvate Dehydrogenase Complex)", "−2.000"], ["", "BAG2 Signaling Pathway", "1.000", "Complement System", "0.816"], ["", "Breast Cancer Regulation by Stathmin1", "−0.477", "Gluconeogenesis I", "1.342"], ["", "Cardiac Hypertrophy Signaling", "1.000", "Glutaryl-CoA Degradation", "−2.236"], ["", "Cardiac Hypertrophy Signaling (Enhanced)", "1.342", "Glycolysis I", "2.000"], ["", "Coagulation System", "−1.342", "Hepatic Fibrosis Signaling Pathway", "1.342"], ["", "Coronavirus Pathogenesis Pathway", "−2.000", "ILK Signaling", "1.732"], ["", "Death Receptor Signaling", "2.000", "Inhibition of ARE-Mediated mRNA Degradation Pathway", "2.236"], ["", "Endocannabinoid Neuronal Synapse Pathway", "1.000", "Intrinsic Prothrombin Activation Pathway", "−0.447"], ["", "Fcγ Receptor-mediated Phagocytosis in Macrophages and Monocytes", "2.000", "Isoleucine Degradation I", "−2.236"], ["", "HIF1α Signaling", "1.000", "Ketogenesis", "−1.342"], ["", "Leukocyte Extravasation Signaling", "2.000", "Ketolysis", "−1.000"], ["", "Necroptosis Signaling Pathway", "0.816", "MSP-RON Signaling in Cancer Cells Pathway", "2.236"], ["", "Opioid Signaling Pathway", "1.000", "Necroptosis Signaling Pathway", "−0.447"], ["", "PPARα/RXRα Activation", "−2.121", "Senescence Pathway", "−1.000"], ["", "RhoA Signaling", "2.236", "Tryptophan Degradation III (Eukaryotic)", "−2.236"], ["", "RhoGDI Signaling", "−2.000", "Valine Degradation I", "−2.646"], ["", "Role of NFAT in Cardiac Hypertrophy", "2.000", "", ""], ["", "Signaling by Rho Family GTPases", "2.449", "", ""], ["", "Unfolded protein response", "2.000", "", ""], ["", "Xenobiotic Metabolism CAR Signaling Pathway", "1.000", "", ""], ["", "Xenobiotic Metabolism PXR Signaling Pathway", "−1.633", "", ""]], "row_count": 65, "column_count": 5, "numeric_cells": 92, "header_rows": 2, "locator": "section[4]/table-wrap[1]#ijms-22-08711-t001"}}, {"id": "asset:table:pmid:34445425:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:30bf4ea450439a87d2c85dde122f9d7133f2bcce1d8247117c6a7b99950315a1", "bytes": 1230, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#ijms-22-08711-t002", "version": null, "note": "List of unique proteins identified in each group in the cross-comparative analysis.", "structure": {"pmcid": "PMC8395861", "section_index": 5, "section_title": "2.3. Cross-Comparative Analysis Identifies Mitochondrial Compartments as the Main Cellular Components of DEPs", "row_count": 3, "column_count": 6}, "table": {"label": "Table 2", "caption": "List of unique proteins identified in each group in the cross-comparative analysis.", "rows": [["Vehicle", "DMB"], ["Day 1", "Day 3", "Day 7", "Day 1", "Day 3", "Day 7"], ["COFA1, COX8B, CTNB1, DCTN2, DUS3, EIF3B, EZRI, FAHD2, HNRPF, IMB1, KCC2D, KINH, LACE1, MARE2, MGDP1, MIC26, NDUC2, PDC6I, PSA7, RAN, RMD1, RS5, SAM50, SEPT2, STX3, TALDO, UBE2N, UBP5, 6PGD, APOC1, ARF4, C4BPA, CFAB, CHIL3, CMC2, CO4B, CRIP1, EGFR, FETUB, GPX41, HRG, ICAL, ITIH3, KLH41, LMOD2, LUM, MYH11, NEDD4, PRS10, PRS6A, RD23B, RS20, RS3, SYDC, TCPH, THTR, TOM1, UN45B, AN32A, CBR1, DHDH, FAHD1, GLRX1, HDHD2, HOT, NUCG, OXND1, PGS2, PIMT, PSA3, SIR5, SPEG, VP26A, CBR4, CLPP, DDX5, GPD1L, KV5AA, LGUL, MAOX, MIME, PYC, VPS29", "CLPP, COX2, NP1L1, TSP1, CX7A2, XDH, FXR1, FBLI1", "NUCG, GLRX3, AKAP9, CAND1, G3BP1, PRELP, VATG1, MYL4, MPPB", "MLRA, MSRB2, PGFS, PSA6, NQO2, LYZ2", "PDK4, LGMN, PMGE, RADI, CX6A1, COX8B, VATA, MTPN, RS3, TCPE, IC1, PSME2, PSMD1, PCBP2, SAM50, UN45B, DDX1, CPT1B, PLST, NAMPT, CAP2, IPYR, MECR, PFKAP, PSD13", "ITIH3, CLPP, YBOX3, TAU, ARC1B, EIF3A, FBN1, NDUB1, PRS8, SYRC, PDK4"]], "row_count": 3, "column_count": 6, "numeric_cells": 8, "header_rows": 2, "locator": "section[5]/table-wrap[1]#ijms-22-08711-t002"}}, {"id": "asset:table:pmid:34445425:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:63aa45cd2357abd22ec4d90ab0057d8193f4a9736aab13afdd9c953a64153b58", "bytes": 563, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#ijms-22-08711-t003", "version": null, "note": "Protein–protein interaction network parameters.", "structure": {"pmcid": "PMC8395861", "section_index": 7, "section_title": "2.5. Protein–Protein Interaction Networks Reveal Dynamic Changes in Protein Expression in Early Remodeling", "row_count": 10, "column_count": 5}, "table": {"label": "Table 3", "caption": "Protein–protein interaction network parameters.", "rows": [["Day", "Total Number of Nodes (Seed + Interacting Partners)", "Number of Interactions", "Unique Proteins and DEPs in Network (Seed Proteins)", "High-Degree Proteins(Unique for That Day)"], ["Day 1", "198", "612", "43", "Fancd2"], ["Atp2a2"], ["Eed"], ["Day 3", "768", "3314", "81", "Fxr1"], ["Fancd2"], ["Actb"], ["Day 7", "922", "4317", "39", "Mapt"], ["Actb"], ["Fancd2"]], "row_count": 10, "column_count": 5, "numeric_cells": 12, "header_rows": 1, "locator": "section[7]/table-wrap[1]#ijms-22-08711-t003"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "network_analysis", "specific": "centrality", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "centrality"}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PXD027867 and 10.6019/PXD027867"], "resolved_accessions": [], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD027867 and 10.6019/PXD027867."], "basis": "The paper names PXD027867 and 10.6019/PXD027867, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:34445425", "asset:table:pmid:34445425:1", "asset:table:pmid:34445425:2", "asset:table:pmid:34445425:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:09Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 38682, "completion_tokens": 1559, "cached_tokens": 792}}, "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:34445425", "type": "paper", "label": "pmid:34445425"}, {"id": "source:pmid:34445425", "type": "manuscript", "label": "PMID 34445425 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34445425", "type": "paper", "label": "pmid:34445425"}, {"id": "source:pmid:34445425", "type": "manuscript", "label": "PMID 34445425 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34445425", "type": "extraction", "used": ["source:pmid:34445425"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:34445425", "parent_hash": "sha256:903b8bf3fde31c13b922ff1f5f149c11becbd4c3848bd9ab9fc01c464438cb0e", "fork_of": null, "generation": 6}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Proteomics of Mouse Heart Ventricles Reveals Mitochondria and Me", "to characterize the range of effects of DMB in vivo throughout the course of early postinfarctio"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}