{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28820483", "kind": "science-record", "revision": 7, "content_hash": "sha256:93bead2563f2a68c52aeafe6e8d76794c956b3f1d7b0e19374eddf8d61b9e20a", "created_at": "2026-11-01T15:40:27Z", "updated_at": "2026-11-01T21:59:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses.", "doi": "10.3390/proteomes5030022", "pmid": "28820483", "authors": ["May Alqurashi", "Ludivine Thomas", "Chris Gehring", "Claudius Marondedze"], "journal": "Proteomes", "year": 2017, "abstract": "The plant hormone abscisic acid (ABA) modulates a number of plant developmental processes and responses to stress. In planta, ABA has been shown to induce reactive oxygen species (ROS) production through the action of plasma membrane-associated nicotinamide adenine dinucleotide phosphate (NADPH)-oxidases. Although quantitative proteomics studies have been performed to identify ABA- or hydrogen peroxide (H₂O₂)-dependent proteins, little is known about the ABA- and H₂O₂-dependent microsomal proteome changes. Here, we examined the effect of 50 µM of either H₂O₂ or ABA on the Arabidopsis microsomal proteome using tandem mass spectrometry and identified 86 specifically H₂O₂-dependent, and 52 specifically ABA-dependent proteins that are differentially expressed. We observed differential accumulation of proteins involved in the tricarboxylic acid (TCA) cycle notably in response to H₂O₂. Of these, aconitase 3 responded to both H₂O₂ and ABA. Additionally, over 30 proteins linked to RNA biology responded significantly to both treatments. Gene ontology categories such as 'response to stress' and 'transport' were enriched, suggesting that H₂O₂ or ABA directly and/or indirectly cause complex and partly overlapping cellular responses. Data are available via ProteomeXchange with identifier PXD006513.", "claims": [{"id": "claim-method", "statement": "Proteins were deemed responsive to treatment when present in at least two replicates with a fold change (FC) greater or equal to |±2|, verified by Student t-test (p-value ≤ 0.05) in comparison to the mock-treated samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28820483", "locator": "sections[5] \"2.3. Trypsin Digestion and Protein Identification by Tandem Mass Spectrometry\" paragraph 2", "quote": "Proteins were deemed responsive to treatment when present in at least two replicates with a fold change (FC) greater or equal to |±2|, verified by Student t-test (p-value ≤ 0.05) in comparison to the mock-treated samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD006513.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28820483", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD006513."}], "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:28820483"], "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:PXD006513"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:PXD006513"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28820483", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/proteomes5030022", "sha256": "sha256:10ba204b6ee0649a538f43bc1c7619d0e6eae98666528d018d69ddcde68b2fed", "bytes": 46421, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/proteomes5030022", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5620539", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD006513", "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=PXD006513", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD006513", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD006513.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD006513.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "A microsomal proteomics view of H2O2- and ABA-dependent responses", "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:28820483:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:65a172c7045d86de7002ccf06427edc4ea59ee36720cf9784953a68cd71dc779", "bytes": 6001, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#proteomes-05-00022-t001", "version": null, "note": "Proteins responsive to H2O2 treatment.", "structure": {"pmcid": "PMC5620539", "section_index": 8, "section_title": "3. Results", "row_count": 99, "column_count": 5}, "table": {"label": "Table 1", "caption": "Proteins responsive to H2O2 treatment.", "rows": [["Accession Number", "Protein Name", "ANOVA (p-Value)", "FC 5 min", "FC 20 min"], ["1. Metabolism"], ["AT1G17745", "D-3-phosphoglycerate dehydrogenase 2", "0.0089", "0.1", "0.1"], ["AT5G26780", "Serine hydroxymethyltransferase 2", "0.036", "2.1", "13"], ["AT3G61440", "Cysteine synthase C1", "0.00074", "ns", "5"], ["AT4G14880", "O-acetylserine (thiol) lyase isoform A1", "0.015", "0.1", "7.9"], ["AT5G23300", "Pyrimidine d", "0.013", "0.2", "ns"], ["AT3G09820", "Adenosine kinase 1", "0.0042", "0.1", "14.0"], ["AT5G17770", "NADH:cytochrome B5 reductase 1", "0.017", "0.4", "2.5"], ["AT1G74790", "Catalytics", "0.045", "5.7", "4.6"], ["AT4G23850", "AMP-dep. synthetase and ligase protein", "0.017", "0.5", "ns"], ["AT1G65290", "Mitochondrial acyl carrier protein 2", "0.044", "2.9", "ns"], ["AT3G47930", "L-galactono-1,4-lactone dehydrogenase", "0.019", "0.2", "ns"], ["2. Energy"], ["AT1G79550", "Phosphoglycerate kinase", "0.0069", "0.2", "2.0"], ["AT1G24180", "Pyruvate dehydrogenase E1 comp. α-2", "0.014", "0.1", "0.2"], ["AT3G48000", "Aldehyde dehydrogenase 2B4", "0.022", "4.3", "7.1"], ["AT3G60750", "Transketolase", "0.0087", "0.5", "4.5"], ["AT2G05710", "Aconitase 3", "0.0002", "2.5", "12.0"], ["AT2G20420", "ATP citrate lyase", "0.022", "ns", "5.0"], ["AT5G08300", "Succinyl-CoA ligase, alpha subunit", "0.006", "2.4", "2.5"], ["AT2G44350", "Citrate synthase family protein", "0.026", "ns", "5.9"], ["AT1G65930", "Cyt. NADP+-dep. isocitrate dehydrogenase", "0.033", "0.1", "2.9"], ["AT1G15120", "Ubiquinol-cytochrome C reductase hinge", "0.016", "19", "20"], ["AT3G03100", "NADH:ubiquinone oxidoreductase,17.2kDa", "0.0029", "0.5", "ns"], ["AT5G13430", "Ubiquinol-cytochrome C reductase, Fe-S", "0.02", "0.2", "ns"], ["AT3G14610", "Cytochrome P450, 72A, polypeptide 7", "0.0026", "0.1", "5.4"], ["3. Cell growth/division"], ["AT5G52240", "Membrane steroid binding protein 1", "0.02", "0.1", "7.5"], ["AT1G10930", "DNA helicase (RECQl4A)", "0.0036", "4.6", "0.1"], ["AT3G44310", "Nitrilase 1", "0.023", "2.9", "ns"], ["4. Transcription"], ["AT1G14850", "Nucleoporin 155", "0.00094", "ns", "0.3"], ["5. Protein synthesis"], ["AT1G01100", "60S acidic ribosomal", "0.022", "ns", "0.4"], ["AT3G48930", "Nucleic acid-binding, OB-fold-like protein", "0.024", "2.1", "ns"], ["AT3G10090", "Nucleic acid-binding, OB-fold-like protein", "0.027", "ns", "0.3"], ["AT3G09200", "Ribosomal protein L10", "0.012", "2.9", "ns"], ["AT3G04400", "Ribosomal protein L14p/L23e", "0.0095", "3.8", "3.0"], ["AT1G23290", "Ribosomal protein L18e/L15", "0.017", "ns", "0.5"], ["AT4G02230", "Ribosomal protein L19e", "0.0089", "ns", "0.3"], ["AT2G44120", "Ribosomal protein L30/L7", "0.027", "ns", "0.5"], ["AT5G56710", "Ribosomal protein L31e", "0.013", "4.6", "ns"], ["AT3G45030", "Ribosomal protein S10p/S20e", "0.03", "ns", "2.2"], ["AT5G02960", "Ribosomal protein S12/S23", "0.016", "2.3", "ns"], ["AT3G60245", "Zinc-binding ribosomal protein", "0.036", "2.4", "ns"], ["6. Protein destination and storage"], ["AT1G14980", "Chaperonin 10", "0.022", "ns", "2.9"], ["AT3G02530", "Chaperonin 60 family protein", "0.045", "2.2", "0.4"], ["AT3G03960", "Chaperonin 60 family protein", "0.041", "2.1", "ns"], ["AT5G56030", "Heat shock protein 81-2", "0.012", "0.4", "ns"], ["AT3G52140", "Tetratricopeptide repeat-containing protein", "0.04", "5.3", "ns"], ["7. Transporters"], ["AT4G38580", "Farnesylated protein 6", "0.017", "0.4", "ns"], ["AT3G15660", "Glutaredoxin 4", "0.011", "ns", "6.0"], ["AT1G27950", "Glycosylphosphatidylinositol-anchored lipid protein transfer 1", "0.027", "16.0", "44.0"], ["AT1G07670", "Endomembrane-type CA-ATPase 4", "0.0026", "0.1", "5.0"], ["AT4G27500", "Proton pump interactor 1", "0.006", "ns", "2.4"], ["AT4G39080", "Vacuolar proton ATPase A3", "0.0041", "0.5", "ns"], ["AT3G58730", "Vacuolar proton pump D subunit", "0.044", "0.4", "ns"], ["AT1G15500", "TLC ATP/ADP transporter", "0.0099", "0.3", "ns"], ["AT4G28390", "ADP/ATP carrier 3", "0.014", "0.1", "ns"], ["AT5G60460", "Preprotein translocase Sec, Sec61-β subunit", "0.0081", "4.7", "4"], ["AT3G51890", "Clathrin light chain protein", "0.019", "ns", "0.5"], ["AT3G08530", "Clathrin, heavy chain", "0.0021", "0.5", "0.2"], ["AT3G11130", "Clathrin, heavy chain", "0.00044", "0.5", "0.4"], ["AT5G19760", "Mitochondrial substrate carrier protein", "0.038", "ns", "2.2"], ["AT5G40810", "Cytochrome C1", "0.021", "0.3", "ns"], ["8. Intracellular traffic"], ["AT3G49560", "Mit. import inner membrane translocase Tim17", "0.0031", "0.1", "ns"], ["AT1G61570", "Mit. import inner membrane translocase 13", "0.0044", "17", "23"], ["AT1G27390", "Translocase outer membrane 20-2", "0.0015", "0.1", "2.1"], ["AT3G60600", "Vesicle associated protein", "0.051", "ns", "3"], ["AT4G34660", "SH3 domain-containing protein", "0.039", "4.7", "ns"], ["9. Cell structure"], ["AT5G09810", "Actin 7", "0.0038", "0.5", "ns"], ["AT5G19770", "Tubulin alpha-3", "0.016", "0.1", "ns"], ["AT5G62690", "Tubulin beta chain 2", "0.006", "0.4", "0.4"], ["AT2G29550", "Tubulin beta-7 chain", "0.0034", "0.3", "0.4"], ["AT4G14960", "Tubulin/FtsZ family protein", "0.036", "0.4", "0.5"], ["AT3G08950", "Electron transport SCO1/SenC protein", "0.045", "0.1", "4.3"], ["10. Signal transduction"], ["AT3G14840", "LRR transmembrane protein kinase", "0.025", "ns", "11"], ["AT5G59840", "Ras-related small GTP-binding protein", "0.0084", "0.1", "2.7"], ["AT3G51800", "Metallopeptidase M24", "0.0015", "5.1", "ns"], ["11. Disease/Defence"], ["AT3G57280", "Transmembrane proteins 14C", "0.014", "0.1", "ns"], ["AT3G12500", "Basic chitinase", "0.035", "ns", "2.1"], ["AT3G32980", "Peroxidase superfamily protein", "0.012", "ns", "3"], ["AT4G36430", "Peroxidase superfamily protein", "0.015", "0.1", "ns"], ["12. Unclassified"], ["AT2G40765", "Unknown protein", "0.019", "2", "ns"], ["AT2G46540", "Unknown protein", "0.033", "ns", "3.5"], ["AT4G12590", "Transmembrane protein, DUF106", "0.033", "0.3", "ns"], ["AT1G08480", "Unknown protein", "0.048", "0.2", "0.4"], ["AT3G20370", "TRAF-like family protein", "0.0058", "0.2", "3"], ["AT3G49720", "Unknown protein", "0.016", "0.1", "0.3"], ["AT4G24330", "DUF1682, unknown protein", "0.0077", "0.1", "2.2"], ["AT2G33585", "Unknown protein", "0.019", "0.1", "13"]], "row_count": 99, "column_count": 5, "numeric_cells": 353, "header_rows": 1, "locator": "section[8]/table-wrap[1]#proteomes-05-00022-t001"}}, {"id": "asset:table:pmid:28820483:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7026578a3d9b8c4ad78965d5c2b77a9432c9e11f75b26965192842224d248f9d", "bytes": 3796, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[2]#proteomes-05-00022-t002", "version": null, "note": "Proteins responsive to abscisic acid (ABA) treatment.", "structure": {"pmcid": "PMC5620539", "section_index": 8, "section_title": "3. Results", "row_count": 64, "column_count": 5}, "table": {"label": "Table 2", "caption": "Proteins responsive to abscisic acid (ABA) treatment.", "rows": [["Accession Number", "Protein Name", "ANOVA (p-Value)", "FC 5 min", "FC 20 min"], ["1. Metabolism"], ["AT2G26400", "Acireductone dioxygenase 3", "0.035", "3.9", "6.8"], ["AT4G34200", "D-3-phosphoglycerate dehydrogenase 1", "0.017", "0.5", "ns"], ["AT1G17745", "D-3-phosphoglycerate dehydrogenase 2", "0.029", "0.1", "0.2"], ["AT4G13940", "S-adenosyl-L-homocysteine hydrolase", "0.028", "2.5", "2.0"], ["AT3G17820", "Glutamine synthetase 1.3", "0.023", "3.7", "3.5"], ["AT5G17770", "NADH cytochrome B5 reductase 1", "0.046", "2.3", "2.3"], ["AT3G15730", "Phospholipase D α 1", "0.014", "3.2", "3.8"], ["2. Energy"], ["AT2G01140", "Aldolase superfamily protein", "0.0075", "5.0", "5.1"], ["AT5G43940", "GroES-like zinc-binding dehydrogenase", "0.014", "4.5", "5.2"], ["AT4G34870", "Rotamase cyclophilin 5", "0.0015", "3.1", "2.7"], ["AT2G05710", "Aconitase 3", "0.035", "8.0", "9.9"], ["AT1G15120", "Ubiquinol-cytochrome C reductase hinge", "0.041", "15.0", "11.0"], ["AT2G33220", "GRIM-19 protein", "0.017", "2.9", "7.1"], ["3. Cell growth/division"], ["AT5G43070", "WPP domain protein 1", "0.042", "0.4", "0.2"], ["4. Transcription"], ["AT2G18740", "Small nuclear ribonucleoprotein", "0.02", "7.7", "4.3"], ["AT5G40480", "Embryo defective 3012", "0.0084", "5.6", "7.9"], ["AT1G14850", "Nucleoporin 155", "0.0058", "0.1", "0.2"], ["5. Protein synthesis"], ["AT1G08360", "Ribosomal protein L1p/L10e", "0.037", "3.1", "ns"], ["AT4G10450", "Ribosomal protein L6", "0.00092", "12.0", ">0.1"], ["AT5G08180", "Ribosomal protein L7Ae", "0.022", "11.0", "8.7"], ["AT3G04400", "Ribosomal protein L14p", "0.016", "3.5", "2.6"], ["AT3G14600", "Ribosomal protein L18ae", "0.033", "3.4", "3.3"], ["AT3G45030", "Ribosomal protein S10p/S20e", "0.0041", "2.3", "ns"], ["AT5G47930", "Zinc-binding ribosomal protein", "0.027", "8.6", "7.0"], ["AT4G00810", "60S acidic ribosomal protein family", "0.042", "0.4", "0.4"], ["AT1G01100", "60S acidic ribosomal protein family", "0.045", "0.4", "0.4"], ["AT5G47700", "60S acidic ribosomal protein family", "0.0085", "0.3", "0.4"], ["6. Protein destination and storage"], ["AT1G14980", "Chaperonin 10", "0.0061", "2.5", "3.0"], ["AT3G16420", "PYK10-binding protein 1", "0.017", "0.3", "0.5"], ["AT5G56030", "Heat shock protein 81-2", "0.0038", "0.4", "0.5"], ["AT1G03220", "Eukaryotic aspartyl protease", "0.0045", "2.3", "2.5"], ["7. Transporters"], ["AT3G53420", "Plasma membrane intrinsic protein 2A", "0.031", "0.3", "ns"], ["AT3G42050", "Vacuolar ATP synthase subunit H", "0.045", "4.4", "4.2"], ["AT4G27500", "Proton pump interactor 1", "0.0048", "ns", "2.3"], ["AT2G34250", "SecY protein transport", "0.011", "2.5", "3.9"], ["AT3G08530", "Clathrin, heavy chain", "0.0019", "0.2", "0.4"], ["AT3G11130", "Clathrin, heavy chain", "0.00054", "0.3", "0.4"], ["8. Intracellular traffic"], ["AT2G29530", "TIM10 zinc finger protein", "0.021", "6.0", "5.0"], ["AT1G61570", "Mit. import inner membrane 13 translocase", "0.042", "19.0", "11.0"], ["9. Cell structure"], ["AT4G30270", "Xyloglucan endotransglucosylase", "0.045", "ns", "3.0"], ["AT3G18780", "Actin 2", "0.016", "0.3", "ns"], ["AT5G09810", "Actin 7", "0.00073", "0.5", "0.5"], ["AT5G19770", "Tubulin alpha-3", "0.044", "0.5", "0.3"], ["AT5G62690", "Tubulin beta chain 2", "0.003", "0.3", "0.4"], ["AT2G29550", "Tubulin beta-7 chain", "0.0072", "0.3", "0.4"], ["AT4G14960", "Tubulin/FtsZ family protein", "0.019", "0.4", "0.3"], ["10. Signal transduction"], ["AT3G14840", "LRR transmembrane protein kinase", "0.014", "8.3", "14.0"], ["AT3G51800", "Metallopeptidase M24", "0.027", "3.4", "ns"], ["11. Disease/Defence"], ["AT1G78850", "D-mannose binding lectin protein", "0.0013", "14.0", "18.0"], ["AT2G43610", "Chitinase family protein", "0.05", "ns", "0.3"], ["AT4G38740", "Rotamase CYP 1", "0.02", "2.6", "ns"], ["AT1G20620", "Catalase 3", "0.0064", "3.5", "2.1"]], "row_count": 64, "column_count": 5, "numeric_cells": 245, "header_rows": 1, "locator": "section[8]/table-wrap[2]#proteomes-05-00022-t002"}}, {"id": "asset:table:pmid:28820483:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:44de3bf261db64b8ca950888ca99709786b25f7370f2a42f2ce7523dfbae36db", "bytes": 1895, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[3]#proteomes-05-00022-t003", "version": null, "note": "Comparison differential protein accumulation in response to ABA and H2O2.", "structure": {"pmcid": "PMC5620539", "section_index": 8, "section_title": "3. Results", "row_count": 31, "column_count": 6}, "table": {"label": "Table 3", "caption": "Comparison differential protein accumulation in response to ABA and H2O2.", "rows": [["Accession Number", "Protein Name", "H2O2 5 min", "H2O2 20 min", "ABA 5 min", "ABA 20 min"], ["1. Metabolism"], ["AT1G17745", "D-3-phosphoglycerate dehydrogenase 2", "0.1", "0.1", "0.1", "0.2"], ["AT5G17770", "NADH:cytochrome B5 reductase 1", "0.4", "2.5", "2.3", "2.3"], ["2. Energy"], ["AT2G05710", "Aconitase 3", "2.5", "12", "8", "9.9"], ["AT1G15120", "Ubiquinol-cytochrome C reductase hinge", "19", "20", "15", "11"], ["3. Transcription"], ["AT1G14850", "Nucleoporin 155", "ns", "0.3", "0.1", "0.2"], ["4. Protein synthesis"], ["AT3G04400", "Ribosomal protein L14p/L23e", "3.8", "3", "3.5", "2.6"], ["AT3G45030", "Ribosomal protein S10p/S20e", "ns", "2.2", "2.3", "ns"], ["AT1G01100", "60S acidic ribosomal protein family", "ns", "0.4", "0.4", "0.4"], ["5. Protein destination and storage"], ["AT1G14980", "Chaperonin 10", "ns", "2.9", "2.5", "3"], ["AT5G56030", "Heat shock protein 81-2", "0.4", "ns", "0.4", "0.5"], ["6. Transporters"], ["AT4G27500", "Proton pump interactor 1", "ns", "2.4", "ns", "2.3"], ["AT3G08530", "Clathrin, heavy chain", "0.5", "0.2", "0.2", "0.4"], ["AT3G11130", "Clathrin, heavy chain", "0.5", "0.4", "0.3", "0.4"], ["7. Intracellular traffic"], ["AT1G61570", "Mit. import inner membrane 13 translocase", "17", "23", "19", "11"], ["8. Cell structure"], ["AT5G09810", "Actin 7", "0.5", "ns", "0.5", "0.5"], ["AT4G14960", "Tubulin/FtsZ family protein", "0.4", "0.5", "0.4", "0.3"], ["AT5G62690", "Tubulin beta chain 2", "0.4", "0.4", "0.3", "0.4"], ["AT2G29550", "Tubulin beta-7 chain", "0.3", "0.4", "0.3", "0.4"], ["AT5G19770", "Tubulin alpha-3", "0.1", "ns", "0.5", "0.3"], ["9. Signal transduction"], ["AT3G51800", "Metallopeptidase M24 family protein", "5.1", "ns", "3.4", "ns"], ["AT3G14840", "LRR transmembrane protein kinase", "ns", "11", "8.3", "14"]], "row_count": 31, "column_count": 6, "numeric_cells": 121, "header_rows": 1, "locator": "section[8]/table-wrap[3]#proteomes-05-00022-t003"}}], "gaps": ["asset:data:geo:PXD006513 not downloaded", "asset:data:geo:PXD006513 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Proteins were deemed responsive to treatment when present in at least two replicates with a fold change (FC) greater or equal to |±2|, verified by Student t-test (p-value ≤ 0.05) in comparison to the mock-treated samples."}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["PXD006513"], "resolved_accessions": ["PXD006513"], "statements": ["Data are available via ProteomeXchange with identifier PXD006513."], "basis": "The paper names PXD006513 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:28820483", "data:geo:PXD006513", "asset:table:pmid:28820483:1", "asset:table:pmid:28820483:2", "asset:table:pmid:28820483:3"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD006513"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:10:00Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 38831, "completion_tokens": 919, "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:28820483", "type": "paper", "label": "pmid:28820483"}, {"id": "source:pmid:28820483", "type": "manuscript", "label": "PMID 28820483 full text"}, {"id": "data:geo:PXD006513", "type": "dataset", "label": "GEO PXD006513"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28820483", "type": "paper", "label": "pmid:28820483"}, {"id": "source:pmid:28820483", "type": "manuscript", "label": "PMID 28820483 full text"}, {"id": "data:geo:PXD006513", "type": "dataset", "label": "GEO PXD006513"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28820483", "type": "extraction", "used": ["source:pmid:28820483"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD006513", "type": "accession_resolution", "used": ["data:geo:PXD006513"], "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:28820483", "parent_hash": "sha256:6b3e8e802ae0694f2a4a25ec533df41d3747ad38a1604dd5dad822637192339a", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD006513 licence not read", "asset:data:geo:PXD006513 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses.", "hate (NADPH)-oxidases. Although quantitative proteomics studies have been performed to identify ABA-", "Arabidopsis microsomal proteome using tandem mass spectrometry and identified 86 specifically H₂O₂-dependen"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Proteins were deemed responsive to treatment when present in at least two replicates with a fold change (FC) greater or equal to |±2|, verified by Student t-test (p-value ≤ 0.05) in comparison to the mock-treated samples."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:47:35+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}}}