{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26322068", "kind": "science-record", "revision": 8, "content_hash": "sha256:d1f9b1f410ebd939c87fbb4c019efda42f01894538c22109cc97a6e3ca154cbb", "created_at": "2026-11-01T15:40:10Z", "updated_at": "2026-11-01T22:42:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "2-DE proteomics analysis of drought treated seedlings of Quercus ilex supports a root active strategy for metabolic adaptation in response to water shortage.", "doi": "10.3389/fpls.2015.00627", "pmid": "26322068", "authors": ["Lyudmila P Simova-Stoilova", "Maria C Romero-Rodríguez", "Rosa Sánchez-Lucas", "Rafael M Navarro-Cerrillo", "J Alberto Medina-Aunon", "Jesús V Jorrín-Novo"], "journal": "Frontiers in plant science", "year": 2015, "abstract": "Holm oak is a dominant tree in the western Mediterranean region. Despite being well adapted to dry hot climate, drought is the main cause of mortality post-transplanting in reforestation programs. An active response to drought is critical for tree establishment and survival. Applying a gel-based proteomic approach, dynamic changes in root proteins of drought treated Quercus ilex subsp. Ballota [Desf.] Samp. seedlings were followed. Water stress was applied on 20 day-old holm oak plantlets by water limitation for a period of 10 and 20 days, each followed by 10 days of recovery. Stress was monitored by changes in water status, plant growth, and electrolyte leakage. Contrary to leaves, holm oak roots responded readily to water shortage at physiological level by growth inhibition, changes in water status and membrane stability. Root proteins were extracted using trichloroacetate/acetone/phenol protocol and separated by two-dimensional electrophoresis. Coomassie colloidal stained gel images were analyzed and spot intensity data subjected to multivariate statistical analysis. Selected consistent spots in three biological replicas, presenting significant changes under stress, were subjected to MALDI-TOF mass spectrometry (peptide mass fingerprinting and MS/MS). For protein identification, combined search was performed with MASCOT search engine over NCBInr Viridiplantae and Uniprot databases. Data are available via ProteomeXchange with identifier PXD002484. Identified proteins were classified into functional groups: metabolism, protein biosynthesis and proteolysis, defense against biotic stress, cellular protection against abiotic stress, intracellular transport. Several enzymes of the carbohydrate metabolism decreased in abundance in roots under drought stress while some related to ATP synthesis and secondary metabolism increased. Results point at active metabolic adjustment and mobilization of the defense system in roots to actively counteract drought stress.", "claims": [{"id": "claim-method", "statement": "Data were statistically analyzed by ANOVA using the following settings: error model max (average, actual), 0.01 proportions of highest variance values to be removed before variance averaging, 10° of freedom for the Bayesian error model, 0.05 FDR threshold, and zero permutations.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26322068", "locator": "sections[6] \"Image analysis and selection of spots of interest\" paragraph 2", "quote": "Data were statistically analyzed by ANOVA using the following settings: error model max (average, actual), 0.01 proportions of highest variance values to be removed before variance averaging, 10° of freedom for the Bayesian error model, 0.05 FDR threshold, and zero permutations."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available with identifier PXD002484.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26322068", "locator": "sections[8] \"Data submission\" paragraph 2", "quote": "Data are available with identifier PXD002484."}], "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:26322068"], "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:PXD002484"], "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:PXD002484"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26322068", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fpls.2015.00627", "sha256": "sha256:e411623ea8a432fda7933e9e026dd68b4709e855cf3899f32861e78478dc93ef", "bytes": 48375, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fpls.2015.00627", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4536546", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD002484", "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=PXD002484", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD002484", "version": null, "note": "Data are available with identifier PXD002484.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available with identifier PXD002484.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "2-DE proteomics analysis of drought treated seedlings of Quercus ilex", "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:26322068:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5c0bf6c3e929378835726e6da87a71b4a267a74c9a265c71a84ff3d4f662adc5", "bytes": 590, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T1", "version": null, "note": "Water deficit (left part), and electrolyte leakage (right part).", "structure": {"pmcid": "PMC4536546", "section_index": 10, "section_title": "Holm oak morphological and physiological response to drought", "row_count": 6, "column_count": 5}, "table": {"label": "Table 1", "caption": "Water deficit (left part), and electrolyte leakage (right part).", "rows": [["Parameter", "Water deficit %", "Relative electrolyte leakage %"], ["Tissue", "Roots", "Leaves", "Root tips", "Leaves"], ["C0", "10.1 ± 3.1", "10.9 ± 1.3", "16.4 ± 9.5", "9.9 ± 2.9"], ["C10", "8.6 ± 4.2", "10.7 ± 1.1", "20.9 ± 6.7", "6.8 ± 1.7"], ["D10", "29.3 ± 6.9", "11.5 ± 1.7", "41.9 ± 4.9", "7.0 ± 0.9"], ["Remark", "3 times increase", "n.s. change", "2 times increase", "n.s. change"]], "row_count": 6, "column_count": 5, "numeric_cells": 16, "header_rows": 2, "locator": "section[10]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:26322068:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:951e67fcc0b0c59d538ee9e04fffe66da5e93d518a1d3f2d868d9f5dda1d883e", "bytes": 696, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T2", "version": null, "note": "Quercus ilex root proteome changes after drought treatment and recovery.", "structure": {"pmcid": "PMC4536546", "section_index": 11, "section_title": "Quercus ilex root proteome changes after drought and recovery", "row_count": 6, "column_count": 7}, "table": {"label": "Table 2", "caption": "Quercus ilex root proteome changes after drought treatment and recovery.", "rows": [["Variants", "Protein yield (μg.g1FW)", "Total number of spots", "Consistent spots", "Number of Variable spots >2-fold/>1.5-fold change", "Spots up under drought >2-fold change/>1.5-fold change", "Spots down under drought >2-fold change/>1.5-fold change"], ["C10", "370", "384", "364", "", "", ""], ["D10", "580", "364", "353", "75/156", "34/75", "41/81"], ["R10", "582", "447", "361", "104/184", "32/66", "72/118"], ["C20", "633", "391", "369", "", "", ""], ["D20", "740", "358", "347", "80/148", "30/58", "50/90"]], "row_count": 6, "column_count": 7, "numeric_cells": 32, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:26322068:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ded6f6594f08d3e2825aaee764534ceab6c91613533a15f6306ed9afe8a4aa85", "bytes": 13853, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T3", "version": null, "note": "Main functional groups and subgroups of identified proteins and the tendencies of changes in individual proteins within groups.", "structure": {"pmcid": "PMC4536546", "section_index": 12, "section_title": "Identification of differently abundant spots and patterns of protein changes", "row_count": 153, "column_count": 11}, "table": {"label": "Table 3", "caption": "Main functional groups and subgroups of identified proteins and the tendencies of changes in individual proteins within groups.", "rows": [["Protein name/Species of closest homology", "SSP", "Accession No.", "Mr/pI", "Mascot scores", "Spot volume ratio changes"], ["", "", "", "Experimental", "Theoretical", "Protein score/C.I", "Total ion score/ C.I.", "D10/C10", "R10/C20", "D20/C20", "C20/C10"], ["GLYCOLYSIS AND GLYOXYLATE BYPASS"], ["Glucose-6-phosphate isomerase", "", "", "", "", "", "", "", "", "", ""], ["Pop.trichocarpa", "1401", "tr|B9GV29|B9GV2", "45.56/5.8", "68.1/5.55", "367/100", "275/100", "1.301", "0.835", "1.415*", "0.914"], ["Phosphofructokinase", "", "", "", "", "", "", "", "", "", ""], ["Citrus paradisi", "4707", "tr|Q9ZST3|Q9ZST", "65.7/6.71", "62.23/6.1", "163/100", "129/100", "0.672*", "0.722", "0.584*", "1.137"], ["Phosphoglycerate mutase", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "1702", "sp|P35493|PMGI_", "70.51/5.9", "61.01/5.5", "249/100", "205/100", "0.532*", "0.356*", "0.312*", "1.086"], ["", "2701", "tr|B9S1V6|B9S1V", "69.86/6.1", "", "306/100", "255/100", "0.549*", "0.813", "0.464*", "0.967"], ["Enolase", "", "", "", "", "", "", "", "", "", ""], ["Jatropha curcas", "1504", "tr|E6NU46|E6NU4", "55.7/5.92", "52.69/6.3", "384/100", "319/100", "1.799", "1.089", "1.719*", "0.911"], ["Spinacia oleracea", "1507", "tr|Q9LEE0|Q9LEE", "55.25/6.0", "48.37/5.5", "187/100", "134/100", "1.121", "0.207*", "0.851", "1.463"], ["Alnus glutinosa", "3503", "sp|Q43321|ENO_A", "56.84/6.4", "47.79/5.4", "460/100", "396/100", "0.746", "1.362", "0.477*", "0.718"], ["Ricinus communis", "5602", "tr|B9R9N6|B9R9N", "58.52/6.8", "48.15/5.7", "461/100", "400/100", "0.243*", "0.409*", "0.181*", "1.099"], ["Glucose-1-phosphate adenylyl transferase", "", "", "", "", "", "", "", "", "", ""], ["Glycine max", "1407", "tr|I1JJP2|I1JJP", "51.01/6.03", "56.71/6.3", "574/100", "445/100", "1.565", "0.393*", "1.413", "1.235"], ["6-phospho-fructokinase 3 PFK3", "", "", "", "", "", "", "", "", "", ""], ["Arabidopsis thaliana", "7605", "sp|Q94AA4|K6PF3", "61.41/7.4", "54.09/6.61", "317/100", "268/100", "0.609", "1.174", "0.578*", "0.964"], ["Phosphoglucomutase", "", "", "", "", "", "", "", "", "", ""], ["Populus tremula", "3707", "sp|Q9ZSQ4|PGMC_", "74.14/6.4", "63.37/5.5", "240/100", "145/100", "", "R+", "", ""], ["Triosephosphate isomerase", "", "", "", "", "", "", "", "", "", ""], ["Solanum tuberosum", "5106", "tr|Q3HRV9|Q3HRV", "20.82/6.8", "27.92/5.9", "378/100", "321/100", "0.564", "0.379*", "0", "2.005*"], ["Malic enzyme", "", "", "", "", "", "", "", "", "", ""], ["Oryza brachyantha", "7701", "tr|J3L3Y9|J3L3Y", "76.28/7.1", "71.65/8.8", "123/100", "116/100", "0", "1.564", "0", "0.99"], ["Fructose-bisphosphate aldolase, cytoplasmic isozyme 2", "", "", "", "", "", "", "", "", "", ""], ["Pisum sativum", "7306", "sp|P46257|ALF2_", "43.39/7.43", "38.64/6.77", "104/100", "83/100", "", "R+", "", ""], ["Aconitate hydratase, cytoplasmic", "", "", "", "", "", "", "", "", "", ""], ["Cucurbita maxima", "5806", "sp|P49608|ACOC_", "98.54/6.9", "98.57/5.7", "166/100", "118/100", "0.441*", "0.948", "0.305*", "1.222"], ["TRICARBOXYLIC ACID CYCLE"], ["Isocitrate dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "2303", "tr|B9SRZ2|B9SRZ", "41.8/6.11", "40.63/7.0", "327/100", "258/100", "1.587*", "0.74", "1.447", "0.712"], ["Pyruvate dehydrogenase E1 beta", "", "", "", "", "", "", "", "", "", ""], ["Pisum sativum", "1201", "sp|P52904|ODPB_", "38.03/5.8", "38.99/5.9", "251/100", "234/100", "1.085", "0.681", "1.522*", "0.811"], ["Dihydrolipoyl lysine-residue acetyltransferase", "", "", "", "", "", "", "", "", "", ""], ["Arabidopsis thaliana", "1502", "sp|Q5M729|OPD23", "54.32/5.8", "58.89/7.9", "350/100", "324/100", "0.743", "0.182*", "0.701", "1.227"], ["AMINO ACID METABOLISM"], ["Glutamine synthetase", "", "", "", "", "", "", "", "", "", ""], ["Camellia sinensis", "3302", "tr|Q762D2|Q762D", "40.11/6.3", "39.41/5.5", "206/100", "188/100", "1.301", "0.751", "1.476*", "0.899"], ["Cysteine synthase", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "2102", "tr|B9RET4|B9RET", "31.66/6.2", "34.44/ 5.5", "409/100", "369/100", "1.255", "1.048", "1.288", "0.671*"], ["Alanine aminotransferase", "", "", "", "", "", "", "", "", "", ""], ["Oryza sativasubsp. japonica", "0606", "tr|Q7X7S9|Q7X7S", "56.56/5.5", "53.77/5.2", "227/100", "199/100", "0.687*", "0.332*", "0.489*", "0.885"], ["3-phosphoglycerate dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "4702", "tr|B9RYA3|B9RYA", "64.92/6.5", "63.35/7.6", "210/100", "162/100", "0.511*", "1.053", "0.94", "1.031"], ["Glutamate dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Populus trichocarpa", "7402", "tr|B9IPQ2|B9IPQ", "45.2/7.15", "44.72/6.84", "338/100", "281/100", "1.729*", "1.555*", "1.308", "1.587*"], ["ONE CARBON METABOLISM"], ["S-adenosylmethionine synthase", "", "", "", "", "", "", "", "", "", ""], ["Camellia sinensis", "2402", "sp|Q9LDQ7|METK_", "48.07/6.1", "43.23/5.3", "555/100", "403/100", "1.401", "0.349", "0.454*", "2.449"], ["Elaeagnus umbellata", "2405", "sp|Q9AT55|METK", "47.84/6.2", "43.56/5.5", "731/100", "563/100", "1.579*", "0.772", "0.674", "1.081"], ["Vit.b12 indep. methionine synthase", "", "", "", "", "", "", "", "", "", ""], ["Pop. trichocarpa", "6801", "tr|B9HQI3|B9HQI", "87.0/6.97", "85.03/6.2", "566/100", "499/100", "2.555", "2.484", "1.998*", "0.889"], ["Formate dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Quercus robur", "7302", "tr|Q7XHJ0|Q7XHJ", "43.52/7.1", "40.85/6.5", "509/100", "365/100", "1.291", "1.299", "0.966", "0.763*"], ["", "7408", "tr|Q7XHJ0|Q7XHJ", "44.88/7.4", "", "489/100", "368/100", "1.587", "2.649*", "1.361", "0.531*"], ["Methylene tetrahydro folate reductase", "", "", "", "", "", "", "", "", "", ""], ["Arabidopsis thaliana", "4704", "sp|O80585|MTHR", "65.2/6.62", "67.39/5.3", "104/100", "95/100", "1.007", "1.274", "0.279*", "1.114"], ["AMINE BIOSYNTHESIS"], ["Betaine aldehyde dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Amaranthus hypochondr.", "1603", "sp|O04895|BADH_", "63.69/5.8", "55.4/5.4", "246/100", "222/100", "1.877*", "0.77", "0.775", "1.009"], ["Corylus heterophylla", "1605", "tr|E9NRZ9|E9NRZ", "63.72/5.9", "55.2/5.44", "152/100", "127/100", "0.677", "0.36", "0.221*", "1.404"], ["ETHANOL FERMENTATION"], ["Pyruvate decarboxylase", "", "", "", "", "", "", "", "", "", ""], ["Prunus armeniaca", "3703", "tr|B0ZS79|B0ZS7", "69.93/6.3", "66.2/5.74", "244/100", "234/100", "0.345*", "1.54", "0.818", "0.451*"], ["", "3705", "", "70.07/6.4", "", "248/100", "230/100", "0.209*", "0.348*", "0", "1.128"], ["SECONDARY METABOLISM"], ["Chalcone synthase", "", "", "", "", "", "", "", "", "", ""], ["Juglans nigra xJuglans regia Malus domestica", "6403", "tr|Q42864|Q4286", "46.52/7.1", "42.9/6.3", "323/100", "235/100", "2.609*", "0.554*", "0.927", "1.317"], ["7401", "tr|B8R6A2|B8R6A", "46.7/7.12", "42.79/5.7", "494/100", "396/100", "2.472*", "0.709", "0.963", "1.252"], ["(+)-Neomenthol dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Arabid.thaliana", "0104", "sp|Q9M2E2|SDR1_", "25.81/5.5", "33.07/5.4", "83/99.97", "68/99.997", "1.342*", "0.407*", "1.556*", "1.067"], ["Caffeoyl CoA 3-O-methyltransferase", "", "", "", "", "", "", "", "", "", ""], ["Betula platyphylla", "0105", "tr|Q5I2D1|Q5I2D", "23.07/5.5", "27.95/5.4", "433/100", "325/100", "1.718*", "0.603*", "1.051", "1.151"], ["Flavanone 3-hydroxylase", "", "", "", "", "", "", "", "", "", ""], ["Ampelopsis grossedentata", "3303", "tr|I6ZTY9|I6ZTY", "40.46/6.4", "41.2/5.3", "840/100", "606/100", "1.994*", "0.449*", "1.106", "1.252"], ["Dihydroflavonol 4-reductase", "", "", "", "", "", "", "", "", "", ""], ["P.suffruticosa", "6304", "tr|G4WCQ6|G4WCQ", "41.6/7.03", "41.4/5.67", "92/99.996", "76/100", "2.738*", "2.012*", "1.594*", "0.731"], ["Shikimate dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Populus trichocarpa", "6601", "tr|B9HSF2|B9HSF", "64.05/6.9", "58.27/5.9", "96/99.998", "80/100", "2.154*", "1.066", "1.105", "0.95"], ["UDP-glucosyl transferase", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "4507", "tr|B9S1I8|B9S1I", "54.8/6.61", "52.97/6.21", "69/99.224", "59/99.987", "0", "0.194*", "0.382*", "1.814*"], ["ATP SYNTHESIS"], ["ATP synthase subunit beta", "", "", "", "", "", "", "", "", "", ""], ["Vitis vinifera", "1601", "tr|F6GTT2|F6GTT", "58.71/5.7", "59.3/5.9", "941/100", "741/100", "1.284", "0.943", "1.724*", "0.963"], ["NADH-ubiquinone oxidoreductase", "", "", "", "", "", "", "", "", "", ""], ["Zea mays", "3806", "tr|B6U2J0|B6U2J", "84.5/6.42", "81.67/6.1", "235/100", "212/100", "1.605*", "0.388*", "0.806", "0.926"], ["Gamma carbonic anhydrase", "", "", "", "", "", "", "", "", "", ""], ["A. thaliana", "5107", "sp|Q9FWR5|GCA1_", "23.46/6.91", "30.12/7.13", "115/100", "94/100", "2.505", "2.939*", "1.991", "0.712"], ["PROTEIN SYNTHESIS"], ["DEAD box RNA helicase", "", "", "", "", "", "", "", "", "", ""], ["Pisum sativum", "1509", "tr|Q8H1A5|Q8H1A", "50.52/5.5", "47.14/5.39", "310/100", "202/100", "1.784*", "0.495", "1.14", "1.509*"], ["Glycyl-tRNA synthetase", "", "", "", "", "", "", "", "", "", ""], ["Arabidopsis lyrata", "3805", "tr|D7KEM8|D7KEM", "78.97/6.5", "82.49/6.43", "443/100", "395/100", "0.411*", "0.558", "0.878", "0.466*"], ["PROTEIN FOLDING/PROCESSING"], ["Groes chaperonin", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "3007", "tr|B9RR63|B9RR6", "19.06/6.3", "26.58/8.89", "86/99.983", "53/99.912", "2.342*", "0.43*", "2.245*", "1.634"], ["Protein disulfide-isomerase", "", "", "", "", "", "", "", "", "", ""], ["Nicotiana tabacum", "1202", "tr|P93358|P9335", "38.81/5.8", "40.08/5.99", "201/100", "180/100", "0.884", "0.409*", "1.2", "0.834"], ["Chaperonin-60kD", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "1701", "tr|B9S582|B9S58", "66.69/5.7", "61.48/6.2", "393/100", "332/100", "0.646", "0.606*", "0.638", "0.987"], ["heat shock protein STI-like", "", "", "", "", "", "", "", "", "", ""], ["Glycine max", "4809", "tr|I1LGM2|I1LGM", "77.99/6.6", "65.86/6.26", "67/98.652", "54/99.95", "0.632*", "0.485*", "0.991", "0.795"], ["", "4810", "tr|I1J9X8|I1J9X", "78.27/6.6", "66.91/6.07", "68/99.023", "50/99.85", "0.405*", "0.414*", "0.912", "0.356*"], ["Chaperonin,TCP-1", "", "", "", "", "", "", "", "", "", ""], ["Malus domestica", "3604", "tr|D9ZJD1|D9ZJD", "63.5/6.33", "57.4/5.6", "292/100", "223/100", "0.398*", "0.379*", "1.254", "1.04"], ["Ricinus communis", "4705", "tr|B9RSN1|B9RSN", "70.46/6.6", "59.56/ 6.08", "362/100", "238/100", "0.917", "0.77", "0.692", "0.854"], ["Ricinus communis", "5701", "tr|B9SUJ3|B9SUJ", "69.96/6.8", "60.64/5.97", "157/100", "135/100", "0.161*", "0.509", "0.462", "1.138"], ["PROTEIN DEGRADATION"], ["Proteasome subunit beta type", "", "", "", "", "", "", "", "", "", ""], ["Glycine max", "2004", "tr|C6SVE5|C6SVE", "18.43/6.2", "25.17/5.3", "651/100", "592/100", "1.363", "0.671", "1.456*", "1.013"], ["Ricinus communis", "5004", "tr|B9SJ80|B9SJ8", "20.5/6.92", "30.6/7.6", "58/90.457", "47/99.745", "1.58*", "1.167", "1.216", "1.133"], ["Picea sitchensis", "7002", "tr|A9NZ27|A9NZ2", "19.97/7.4", "29.59/5.58", "224/100", "203/100", "1.281", "1.723*", "0.903", "0.951"], ["Xaa-Pro aminopeptidase", "", "", "", "", "", "", "", "", "", ""], ["Solanum lycopersicum", "3803", "tr|Q93X46|Q93X4", "79.52/6.4", "73.45/5.98", "88/99.99", "81/100", "1.58", "1.776*", "1.341", "0.923"], ["Mitochondrial processing peptidase", "", "", "", "", "", "", "", "", "", ""], ["Cucumis melo", "3607", "tr|Q9AXQ2|Q9AXQ", "62.57/6.5", "58.9/6.56", "656/100", "575/100", "1.25", "0.703*", "1.22*", "0.894"], ["Leucine aminopeptidase", "", "", "", "", "", "", "", "", "", ""], ["Medicago truncatula", "2603", "tr|G7JGP9|G7JGP", "58.61/6.1", "59.86/7.56", "292/100", "220/100", "0.577", "0.252*", "0.363*", "1.152"], ["26S protease regulatory subunit 6B", "", "", "", "", "", "", "", "", "", ""], ["M. truncatula", "1402", "tr|G7IV48|G7IV4", "51.86/5.9", "46.58/5.4", "540/100", "335/100", "0.786", "0.552*", "0.673*", "1.322*"], ["Ubiquitin-activating enzyme E1", "", "", "", "", "", "", "", "", "", ""], ["Ric.communis", "1901", "tr|B9SKZ1|B9SKZ", "117.4/5.8", "123.59/5.0", "87/99.988", "67/99.997", "2.059*", "0.758*", "0", "2.624*"], ["STRESS RESPONSE"], ["Aldo/keto reductase", "", "", "", "", "", "", "", "", "", ""], ["Manihot esculenta", "0203", "tr|Q52QX9|Q52QX", "35.02/5.6", "", "232/100", "210/100", "4.2*", "1.116", "2.516*", "1.422"], ["", "3205", "tr|Q52QX9|Q52QX", "38.15/6.3", "38.03/6.38", "325/100", "246/100", "2.025*", "0.785", "2.41*", "0.738"], ["", "4201", "tr|Q52QX9|Q52QX", "38.37/6.51", "", "327/100", "296/100", "0.341*", "0.178*", "1.203", "1.444"], ["Alcohol dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Pyrus communis", "6302", "tr|G0Z9K2|G0Z9K", "41.76/6.9", "42.08/6.51", "611/100", "545/100", "0.119*", "1.149", "0.091", "0.889"], ["Short-chain dehydrogenase / reductase (SDR) family protein", "", "", "", "", "", "", "", "", "", ""], ["Solanum lycopers.", "0103", "tr|K4AZG5|K4AZG", "25.77/5.4", "35.46/5.39", "82/99.95", "78/100", "1.066", "0.323*", "1.185", "1.675*"], ["Aldehyde dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Vitis vinifera", "6602", "tr|G9HQG0|G9HQG", "60.16/6.98", "52.53/6.18", "77/99.86", "63/99.993", "0.464*", "1.572*", "0.668", "1.039"], ["Peroxidase", "", "", "", "", "", "", "", "", "", ""], ["Linum usitatissimum", "0507", "tr|Q43782|Q4378", "48.17/5.4", "38.63/8.07", "77/99.865", "68/99.997", "0.332*", "0.406*", "3.295*", "0.96"], ["Stem-specific protein TSJT1", "", "", "", "", "", "", "", "", "", ""], ["Ricinus Communis", "0005", "tr|B9RTW0|B9RTW", "20.5/5.54", "25.5/5.56", "77/99.87", "70/99.998", "0.189*", "0.451*", "0.906", "1.298"], ["Hypersensitive induced response protein 3", "", "", "", "", "", "", "", "", "", ""], ["Triticum aestivum", "0108", "tr|B6D9L4|B6D9L", "24.68/5.67", "31.8/5.68", "231/100", "202/100", "0.395*", "1.238", "2.499*", "0.949"], ["Al induced protein", "", "", "", "", "", "", "", "", "", ""], ["Arabidopsis thaliana", "2105", "tr|Q9LIL3|Q9LIL", "22.29/5.96", "27.5/5.84", "94/99.997", "85/100", "0.179*", "0.837", "0.755", "0.305*"], ["CELL MOTILITY"], ["Actin 2", "", "", "", "", "", "", "", "", "", ""], ["Gossypium hirsutum", "0404", "tr|B8YPL4|B8YPL", "45.11/5.7", "41.94/5.38", "787/100", "597/100", "1.552", "1.01", "1.804*", "1.052"], ["Annona cherimola", "0703", "tr|H9A1W7|H9A1W", "65.5/5.51", "41.85/5.31", "788/100", "562/100", "0", "0.411", "0", "2.661"], ["PHOTOSYNTHESIS"], ["PsbP domain-containing protein", "", "", "", "", "", "", "", "", "", ""], ["M. truncatula", "0113", "tr|G7J6G5|G7J6G", "26.71/5.3", "27.95/6.92", "62/95.93", "55/99.96", "0.514", "0.056*", "0.889", "3.077"], ["Oxygen-evolving enhancer protein", "", "", "", "", "", "", "", "", "", ""], ["Populus euphratica", "0109", "sp|P84989|PSBO_", "24.86/5.5", "10.6/5.36", "423/100", "361/100", "0", "1.935", "5.33*", "0.605"], ["Rubisco LS", "", "", "", "", "", "", "", "", "", ""], ["Noronhia emarginata", "3706", "tr|Q06QN8|Q06QN", "66.65/6.4", "53.05/6.22", "197/100", "101/100", "0.354*", "0.727", "0", "0.825"]], "row_count": 153, "column_count": 11, "numeric_cells": 726, "header_rows": 2, "locator": "section[12]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:PXD002484 not downloaded", "asset:data:geo:PXD002484 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Data were statistically analyzed by ANOVA using the following settings: error model max (average, actual), 0.01 proportions of highest variance values to be removed before variance averaging, 10° of freedom for the Bayesian error model, 0.05 FDR threshold, and zero permutations."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD002484"], "resolved_accessions": ["PXD002484"], "statements": ["Data are available with identifier PXD002484."], "basis": "The paper names PXD002484 in ProteomeXchange repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:26322068", "data:geo:PXD002484", "asset:table:pmid:26322068:1", "asset:table:pmid:26322068:2", "asset:table:pmid:26322068:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD002484"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "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:26322068", "type": "paper", "label": "pmid:26322068"}, {"id": "source:pmid:26322068", "type": "manuscript", "label": "PMID 26322068 full text"}, {"id": "data:geo:PXD002484", "type": "dataset", "label": "GEO PXD002484"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26322068", "type": "paper", "label": "pmid:26322068"}, {"id": "source:pmid:26322068", "type": "manuscript", "label": "PMID 26322068 full text"}, {"id": "data:geo:PXD002484", "type": "dataset", "label": "GEO PXD002484"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26322068", "type": "extraction", "used": ["source:pmid:26322068"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD002484", "type": "accession_resolution", "used": ["data:geo:PXD002484"], "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:26322068", "parent_hash": "sha256:61c317c3acf12bfde97ebdb633c43590545b91571c831717ecd935fc8139136f", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD002484 licence not read", "asset:data:geo:PXD002484 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Data were statistically analyzed by ANOVA using the following settings: error model max (average, actual), 0.01 proportions of highest variance values to be removed before variance averaging, 10° of freedom for the Bayesian error model, 0.05 FDR threshold, and zero permutations."], "order_basis": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:52:26+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}}}