{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26193361", "kind": "science-record", "revision": 6, "content_hash": "sha256:4d707eb912a57d3a30feb2f7193fa317221a59fbeda969b9583da7fd2c3d4e19", "created_at": "2026-11-01T15:40:09Z", "updated_at": "2026-11-01T21:20:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic Characterisation of the Salt Gland-Enriched Tissues of the Mangrove Tree Species Avicennia officinalis.", "doi": "10.1371/journal.pone.0133386", "pmid": "26193361", "authors": ["Wee-Kee Tan", "Teck-Kwang Lim", "Chiang-Shiong Loh", "Prakash Kumar", "Qingsong Lin"], "journal": "PloS one", "year": 2015, "abstract": "Plant salt glands are nature's desalination devices that harbour potentially useful information pertaining to salt and water transport during secretion. As part of the program toward deciphering secretion mechanisms in salt glands, we used shotgun proteomics to compare the protein profiles of salt gland-enriched (isolated epidermal peels) and salt gland-deprived (mesophyll) tissues of the mangrove species Avicennia officinalis. The purpose of the work is to identify proteins that are present in the salt gland-enriched tissues. An average of 2189 and 977 proteins were identified from the epidermal peel and mesophyll tissues, respectively. Among these, 2188 proteins were identified in salt gland-enriched tissues and a total of 1032 selected proteins were categorized by Gene Ontology (GO) analysis. This paper reports for the first time the proteomic analysis of salt gland-enriched tissues of a mangrove tree species. Candidate proteins that may play a role in the desalination process of the mangrove salt glands and their potential localization were identified. Information obtained from this study paves the way for future proteomic research aiming at elucidating the molecular mechanism underlying secretion in plant salt glands. The data have been deposited to the ProteomeXchange with identifier PXD000771.", "claims": [{"id": "claim-method", "statement": "Identified proteins for each biological replicate were selected based on a false discovery rate (FDR) of < 1%.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26193361", "locator": "sections[4] \"Sample preparation and LC-MS/MS analysis\" paragraph 5", "quote": "Identified proteins for each biological replicate were selected based on a false discovery rate (FDR) of < 1%."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000771.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26193361", "locator": "sections[10] \"Data Availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000771."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used nwCompare to identify proteins found in salt gland-enriched epidermal peels but not mesophyll, yielding 2,188 salt gland-enriched proteins, with the underlying proteomics data deposited in ProteomeXchange under PXD000771.", "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:26193361"], "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:PXD000771"], "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:PXD000771"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26193361", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0133386", "sha256": "sha256:6157b9b36a01a97174d03e47ab847749a08580c547cee7a5c06e40504a2660f5", "bytes": 36754, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0133386", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4508094", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD000771", "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=PXD000771", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000771", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000771.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000771.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic characterisation of the salt gland-enriched tissues of the mangrove tree species Avicennia officinalis", "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:26193361:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4a047fb0a98584f74f99587cbaf77672a9448f0ca1caa11fc275c60f7671fc41", "bytes": 400, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#pone.0133386.t001", "version": null, "note": "Number of proteins identified from adaxial (upper) epidermal peels and mesophyll tissues of the leaves of A. officinalis.", "structure": {"pmcid": "PMC4508094", "section_index": 5, "section_title": "Results", "row_count": 3, "column_count": 2}, "table": {"label": "Table 1", "caption": "Number of proteins identified from adaxial (upper) epidermal peels and mesophyll tissues of the leaves of A. officinalis.", "rows": [["", "Average no. of proteins identified (±SE)"], ["Epidermal peels", "2189 ± 128"], ["Mesophyll tissues", "977 ± 150"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[5]/table-wrap[1]#pone.0133386.t001"}}, {"id": "asset:table:pmid:26193361:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7ac2f9e3d0309441a3b7b233a281577955decbb1d67e2a2a5961fd407365f3c5", "bytes": 19687, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#pone.0133386.t002", "version": null, "note": "Selected list of proteins identified from salt gland-enriched epidermal tissues of A. officinalis.These proteins are identified in the epidermal tissues but not in the mesophyll tissues of A. officinalis and only those that are present in two out of the three biological replicates are selected for further anlaysis. The full list of proteins is presented in S8 Table.", "structure": {"pmcid": "PMC4508094", "section_index": 5, "section_title": "Results", "row_count": 117, "column_count": 15}, "table": {"label": "Table 2", "caption": "Selected list of proteins identified from salt gland-enriched epidermal tissues of A. officinalis.These proteins are identified in the epidermal tissues but not in the mesophyll tissues of A. officinalis and only those that are present in two out of the three biological replicates are selected for further anlaysis. The full list of proteins is presented in S8 Table.", "rows": [["", "", "", "", "Unused ProtScore*", "% Coverage #", "Peptides (95%) ^", "", ""], ["No.", "gi Acession No.", "Swiss-Prot ID", "Contig No.", "T1", "T2", "T3", "T1", "T2", "T3", "T1", "T2", "T3", "Protein Description", "Species"], ["1", "gi|3912949", "O49996", "CL15843.Contig3_All", "2.27", "8.00", "12.21", "42.90", "34.30", "52.70", "6", "5", "9", "14-3-3-like protein D", "Nicotiana tabacum"], ["2", "gi|224136700", "Q9LT08", "CL5021.Contig4_All", "7.70", "3.95", "4.36", "32.10", "33.00", "22.10", "6", "4", "3", "26S proteasome non-ATPase regulatory subunit 14", "Arabidopsis thaliana"], ["3", "gi|3914467", "P93768", "Unigene16875_All", "2.00", "2.00", "0.36", "30.30", "30.30", "30.30", "1", "1", "1", "26S proteasome non-ATPase regulatory subunit 3", "Nicotiana tabacum"], ["4", "gi|350538091", "O04059", "CL2261.Contig1_All", "7.52", "11.08", "6.18", "22.30", "19.20", "20.80", "5", "6", "3", "3,4-dihydroxy-2-butanone kinase", "Solanum lycopersicum"], ["5", "gi|255584390", "Q9LVM1", "CL12689.Contig2_All", "0.91", "2.66", "2.00", "8.90", "13.80", "15.40", "2", "1", "1", "ABC transporter B family member 25", "Arabidopsis thaliana"], ["6", "gi|255552969", "Q9M1H3", "Unigene32800_All", "4.88", "5.62", "2.01", "18.40", "17.60", "18.20", "4", "3", "1", "ABC transporter F family member 4", "Arabidopsis thaliana"], ["7", "gi|296090419", "Q7PC87", "CL4209.Contig1_All", "4.00", "2.01", "21.16", "44.40", "46.80", "53.60", "8", "10", "13", "ABC transporter G family member 34", "Arabidopsis thaliana"], ["8", "gi|359484370", "Q8RXE7", "Unigene4379_All", "4.83", "2.00", "2.18", "19.20", "15.10", "13.60", "3", "1", "1", "ADP-ribosylation factor GTPase-activating protein AGD14", "Arabidopsis thaliana"], ["9", "gi|255546541", "Q56YU0", "CL13289.Contig1_All", "3.08", "4.09", "6.02", "21.10", "25.90", "19.70", "3", "3", "3", "Aldehyde dehydrogenase family 2 member C4", "Arabidopsis thaliana"], ["10", "gi|297823651", "Q0PGJ6", "CL5791.Contig3_All", "4.87", "8.40", "9.74", "39.20", "47.70", "52.30", "6", "7", "7", "Aldo-keto reductase family 4 member C9", "Arabidopsis thaliana"], ["11", "gi|50345961", "Q7XSQ9", "CL16514.Contig4_All", "4.00", "4.01", "6.03", "39.50", "43.00", "36.00", "12", "12", "22", "Aquaporin PIP1-2", "Oryza sativa subsp. japonica"], ["12", "gi|17940742", "Q7XLR1", "Unigene32737_All", "4.00", "2.09", "2.00", "29.60", "33.70", "27.60", "7", "5", "4", "Aquaporin PIP2-6", "Oryza sativa subsp. japonica"], ["13", "gi|255541428", "", "CL8427.Contig3_All", "4.09", "4.00", "2.00", "16.40", "11.60", "6.20", "4", "2", "1", "Arsenical pump-driving atpase", "Ricinus communis"], ["14", "gi|2493046", "Q40089", "CL7437.Contig2_All", "6.89", "5.65", "12.70", "26.10", "46.80", "53.70", "4", "5", "9", "ATP synthase subunit delta'", "Ipomoea batatas"], ["15", "gi|225454791", "", "Unigene6969_All", "3.38", "4.00", "1.54", "47.10", "40.20", "14.90", "2", "2", "1", "ATPase family AAA domain-containing protein 3-B", "Vitis vinifera"], ["16", "gi|224145672", "P28583", "CL274.Contig2_All", "2.39", "1.27", "1.27", "15.50", "22.00", "17.40", "1", "1", "1", "Calcium-dependent protein kinase SK5", "Glycine max"], ["17", "gi|225466204", "Q9CAL3", "CL14803.Contig3_All", "4.96", "4.87", "8.92", "18.60", "22.90", "23.10", "3", "3", "5", "Cysteine-rich receptor-like protein kinase 2", "Arabidopsis thaliana"], ["18", "gi|225452304", "Q93ZC9", "Unigene4267_All", "2.33", "3.39", "4.71", "12.10", "11.20", "34.00", "1", "2", "3", "Glucuronokinase 1", "Arabidopsis thaliana"], ["19", "gi|225445585", "", "CL12018.Contig2_All", "3.12", "2.33", "2.04", "16.20", "15.80", "12.00", "3", "1", "1", "GTPase-activating protein gyp7-like", "Vitis vinifera"], ["20", "gi|351721140", "O64477", "Unigene30402_All", "2.03", "2.92", "3.18", "10.10", "14.00", "11.90", "1", "2", "2", "G-type lectin S-receptor-like serine/threonine-protein kinase At2g19130", "Arabidopsis thaliana"], ["21", "gi|296081939", "F4JMJ1", "CL2876.Contig1_All", "13.17", "7.78", "18.76", "40.10", "32.60", "41.30", "11", "7", "10", "Heat shock 70 kDa protein 17", "Arabidopsis thaliana"], ["22", "gi|224099789", "Q9SKY8", "CL2714.Contig2_All", "4.14", "2.01", "2.44", "17.60", "4.20", "9.10", "2", "1", "1", "Heat shock 70 kDa protein 8", "Arabidopsis thaliana"], ["23", "gi|45331281", "P09189", "CL2270.Contig3_All", "6.03", "4.34", "8.12", "56.00", "52.10", "59.00", "32", "33", "41", "Heat shock cognate 70 kDa protein", "Petunia hybrida"], ["24", "gi|240255879", "", "CL2610.Contig2_All", "4.06", "4.00", "6.00", "44.80", "44.80", "63.20", "2", "2", "3", "Heat shock factor binding protein", "Arabidopsis thaliana"], ["25", "gi|356540381", "Q43468", "CL13990.Contig2_All", "2.09", "6.00", "2.03", "53.40", "52.30", "40.40", "4", "4", "3", "Heat shock protein STI", "Glycine max"], ["26", "gi|359473854", "", "Unigene32812_All", "2.14", "2.09", "4.00", "28.70", "25.30", "14.30", "2", "1", "2", "hsp70 nucleotide exchange factor FES1", "Vitis vinifera"], ["27", "gi|297793865", "Q9FM19", "Unigene2776_All", "3.72", "3.91", "9.97", "32.20", "40.10", "40.80", "6", "7", "11", "Hypersensitive-induced response protein 1", "Arabidopsis thaliana"], ["28", "gi|255576916", "O48788", "Unigene6256_All", "3.02", "2.41", "2.00", "27.50", "27.50", "24.40", "4", "4", "2", "Inactive receptor kinase At2g26730", "Arabidopsis thaliana"], ["29", "gi|2208908", "Q96303", "CL8176.Contig2_All", "12.13", "12.15", "4.64", "18.10", "17.50", "21.40", "9", "8", "7", "Inorganic phosphate transporter 1–4", "Arabidopsis thaliana"], ["30", "gi|357440961", "Q8GYF4", "CL8176.Contig4_All", "6.32", "6.68", "10.07", "19.80", "18.50", "22.20", "7", "6", "6", "Inorganic phosphate transporter 1–5", "Arabidopsis thaliana"], ["31", "gi|297740564", "C0LGE0", "CL3330.Contig3_All", "20.94", "18.55", "25.32", "29.50", "26.70", "31.40", "13", "12", "17", "LRR receptor-like serine/threonine-protein kinase At1g07650", "Arabidopsis thaliana"], ["32", "gi|224112549", "C0LGG9", "Unigene4496_All", "2.01", "2.05", "2.00", "22.00", "26.00", "17.10", "2", "2", "1", "LRR receptor-like serine/threonine-protein kinase At1g53440", "Arabidopsis thaliana"], ["33", "gi|359485959", "C0LGH3", "CL2732.Contig3_All", "4.65", "7.56", "5.09", "25.50", "15.20", "18.80", "4", "4", "4", "LRR receptor-like serine/threonine-protein kinase At1g56140", "Arabidopsis thaliana"], ["34", "gi|359493576", "C0LGQ5", "Unigene30432_All", "6.19", "5.03", "11.29", "31.70", "27.00", "34.60", "5", "4", "7", "LRR receptor-like serine/threonine-protein kinase GSO1", "Arabidopsis thaliana"], ["35", "gi|225444063", "", "CL8211.Contig2_All", "12.44", "7.93", "11.21", "33.80", "29.40", "37.30", "7", "4", "8", "obg-like ATPase 1", "Vitis vinifera"], ["36", "gi|13785471", "Q9T074", "CL2927.Contig4_All", "22.73", "13.53", "24.38", "36.50", "26.90", "40.80", "17", "8", "16", "Phosphoenolpyruvate carboxykinase [ATP]", "Arabidopsis thaliana"], ["37", "gi|225442595", "Q66GQ3", "CL2133.Contig8_All", "9.92", "12.24", "17.14", "33.00", "34.90", "32.50", "5", "8", "11", "Protein disulfide isomerase-like 1–6", "Arabidopsis thaliana"], ["38", "gi|225459342", "Q69SA9", "CL4543.Contig4_All", "0.86", "2.84", "2.29", "22.20", "29.60", "22.20", "1", "2", "2", "Protein disulfide isomerase-like 5–4", "Oryza sativa subsp. japonica"], ["39", "gi|359494074", "", "CL2740.Contig3_All", "2.01", "6.22", "4.06", "39.20", "60.80", "46.00", "6", "4", "6", "Protein grpE-like", "Vitis vinifera"], ["40", "gi|45433315", "P31569", "CL4418.Contig4_All", "4.00", "1.76", "3.06", "29.60", "30.10", "23.60", "6", "5", "6", "Protein ycf2", "Oenothera villaricae"], ["41", "gi|357445105", "B9DFG5", "Unigene196_All", "2.00", "6.02", "7.52", "22.80", "20.10", "41.40", "6", "4", "4", "PTI1-like tyrosine-protein kinase 3", "Arabidopsis thaliana"], ["42", "gi|242064260", "Q06572", "CL6187.Contig3_All", "4.00", "4.01", "2.00", "10.10", "32.40", "26.30", "2", "3", "1", "Pyrophosphate-energized vacuolar membrane proton pump", "Hordeum vulgare"], ["43", "gi|356526237", "P31414", "CL3527.Contig3_All", "2.01", "2.00", "4.35", "11.00", "39.70", "37.00", "2", "2", "4", "Pyrophosphate-energized vacuolar membrane proton pump 1", "Arabidopsis thaliana"], ["44", "gi|359477316", "Q42736", "CL384.Contig14_All", "4.08", "10.48", "2.04", "18.90", "21.00", "21.80", "6", "6", "6", "Pyruvate, phosphate dikinase", "Flaveria pringlei"], ["45", "gi|258678027", "Q9M651", "CL13915.Contig4_All", "1.19", "2.01", "2.00", "25.60", "31.80", "18.50", "1", "1", "1", "RAN GTPase-activating protein 2", "Arabidopsis thaliana"], ["46", "gi|7672732", "P43298", "CL15187.Contig2_All", "3.87", "4.05", "6.86", "15.10", "17.60", "12.40", "3", "2", "4", "Receptor protein kinase TMK1", "Arabidopsis thaliana"], ["47", "gi|224087891", "Q9SCZ4", "CL2320.Contig9_All", "2.00", "1.42", "2.00", "8.20", "9.50", "6.70", "1", "1", "1", "Receptor-like protein kinase FERONIA", "Arabidopsis thaliana"], ["48", "gi|225427230", "Q944A7", "CL5141.Contig1_All", "4.19", "5.46", "1.57", "28.10", "22.00", "21.30", "4", "3", "1", "Serine/threonine-protein kinase At4g35230", "Arabidopsis thaliana"], ["49", "gi|225426412", "Q9FHD7", "CL7376.Contig1_All", "2.59", "7.34", "8.62", "11.30", "25.50", "25.70", "3", "4", "5", "Serine/threonine-protein kinase At5g41260", "Arabidopsis thaliana"], ["50", "gi|145327199", "Q9CAR3", "CL8777.Contig2_All", "2.73", "2.08", "2.00", "13.80", "12.90", "18.40", "2", "1", "1", "SNF1-related protein kinase regulatory subunit gamma-1-like", "Arabidopsis thaliana"], ["51", "gi|194696644", "Q84TI7", "Unigene26174_All", "2.57", "2.20", "2.51", "24.30", "38.60", "37.10", "1", "1", "1", "Sodium transporter HKT1", "Arabidopsis thaliana"], ["52", "gi|359495505", "Q9LRB0", "CL315.Contig4_All", "2.00", "0.74", "2.00", "11.60", "17.60", "6.80", "1", "1", "1", "Sphingoid long-chain bases kinase 1", "Arabidopsis thaliana"], ["53", "gi|225443039", "", "CL10751.Contig1_All", "2.00", "2.00", "2.00", "5.20", "12.30", "11.90", "1", "1", "1", "Uncharacterized membrane protein YMR155W", "Vitis vinifera"], ["54", "gi|255542872", "Q8LGG8", "Unigene11881_All", "0.73", "1.41", "2.00", "12.00", "16.40", "22.00", "1", "2", "2", "Universal stress protein A-like protein", "Arabidopsis thaliana"], ["55", "gi|255556366", "Q8LGG8", "Unigene2529_All", "11.58", "1.08", "10.10", "54.80", "36.90", "38.20", "9", "5", "7", "Universal stress protein A-like protein", "Arabidopsis thaliana"], ["56", "gi|255554204", "O23016", "CL6704.Contig3_All", "2.99", "3.24", "2.35", "23.20", "23.80", "19.20", "2", "2", "2", "Voltage-gated potassium channel subunit beta", "Arabidopsis thaliana"], ["57", "gi|357501685", "Q9LHA4", "CL3237.Contig3_All", "9.72", "1.48", "12.15", "18.50", "22.50", "21.70", "6", "6", "6", "V-type proton ATPase subunit d2", "Arabidopsis thaliana"], ["58", "gi|225463325", "Q9ZQX4", "Unigene24187_All", "8.32", "11.16", "9.34", "43.90", "50.00", "38.50", "5", "7", "6", "V-type proton ATPase subunit F", "Arabidopsis thaliana"], ["59", "gi|225432878", "Q0WNY5", "CL3494.Contig3_All", "6.01", "5.30", "5.91", "21.00", "22.10", "20.80", "3", "4", "3", "Wall-associated receptor kinase-like 18", "Arabidopsis thaliana"], ["60", "gi|124221924", "Q9LZM4", "CL6319.Contig3_All", "15.22", "6.29", "8.21", "23.30", "24.50", "28.10", "7", "3", "6", "Wall-associated receptor kinase-like 20", "Arabidopsis thaliana"], ["61", "gi|255569405", "Q8RXN0", "CL4681.Contig3_All", "6.01", "1.81", "", "18.60", "15.70", "", "3", "1", "", "ABC transporter G family member 11", "Arabidopsis thaliana"], ["62", "gi|171854675", "P49608", "CL2995.Contig26_All", "2.00", "2.00", "", "29.80", "14.60", "", "1", "1", "", "Aconitate hydratase", "Cucurbita maxima"], ["63", "gi|18076583", "Q8S9L6", "CL9653.Contig1_All", "2.00", "2.01", "", "9.90", "11.00", "", "1", "1", "", "Cysteine-rich receptor-like protein kinase 29", "Arabidopsis thaliana"], ["64", "gi|225445342", "", "CL13252.Contig2_All", "0.85", "3.64", "", "10.50", "7.40", "", "2", "4", "", "dnaJ homolog subfamily C member 13-like", "Vitis vinifera"], ["65", "gi|255556438", "Q9SEE5", "Unigene35913_All", "2.00", "2.00", "", "18.40", "22.60", "", "3", "3", "", "Galactokinase", "Arabidopsis thaliana"], ["66", "gi|225463623", "", "CL14543.Contig1_All", "3.87", "1.70", "", "18.30", "9.00", "", "3", "2", "", "Glycerol kinase isoform 1", "Vitis vinifera"], ["67", "gi|359497728", "Q9ASS4", "CL4159.Contig1_All", "2.22", "3.37", "", "21.00", "24.50", "", "3", "3", "", "Inactive leucine-rich repeat receptor-like protein kinase At5g48380", "Arabidopsis thaliana"], ["68", "gi|255552774", "O04567", "Unigene22230_All", "1.41", "0.55", "", "8.60", "19.50", "", "1", "2", "", "Inactive receptor kinase At1g27190", "Arabidopsis thaliana"], ["69", "gi|255586379", "Q9LVM0", "CL2318.Contig1_All", "2.00", "3.46", "", "13.80", "17.10", "", "1", "2", "", "Inactive receptor kinase At5g58300", "Arabidopsis thaliana"], ["70", "gi|225423806", "Q9LI83", "CL3370.Contig1_All", "2.00", "1.61", "", "8.90", "8.20", "", "1", "1", "", "Phospholipid-transporting ATPase 10", "Arabidopsis thaliana"], ["71", "gi|359485026", "Q03194", "CL16623.Contig1_All", "2.16", "0.83", "", "24.60", "18.20", "", "3", "2", "", "Plasma membrane ATPase 4", "Nicotiana plumbaginifolia"], ["72", "gi|125535713", "Q2QY12", "Unigene37237_All", "0.79", "2.00", "", "28.40", "35.80", "", "1", "1", "", "Plasma membrane-type calcium-transporting ATPase 4", "Oryza sativa subsp. japonica"], ["73", "gi|225448277", "Q9FY75", "CL2807.Contig2_All", "2.04", "2.02", "", "4.90", "4.90", "", "1", "1", "", "Potassium transporter 7", "Arabidopsis thaliana"], ["74", "gi|147768303", "Q2MHE4", "CL2457.Contig4_All", "3.92", "1.82", "", "29.10", "12.60", "", "2", "1", "", "Serine/threonine-protein kinase HT1", "Arabidopsis thaliana"], ["75", "gi|255540259", "Q8LBB2", "CL2181.Contig2_All", "4.97", "3.84", "", "22.30", "25.40", "", "3", "2", "", "SNF1-related protein kinase regulatory subunit gamma-1", "Arabidopsis thaliana"], ["76", "gi|350535282", "Q9LKW9", "Unigene18167_All", "2.00", "2.00", "", "21.30", "12.60", "", "1", "1", "", "Sodium/hydrogen exchanger 7", "Arabidopsis thaliana"], ["77", "gi|224141283", "Q8LGG8", "CL2994.Contig3_All", "2.00", "2.20", "", "16.60", "14.90", "", "1", "1", "", "Universal stress protein A-like protein", "Arabidopsis thaliana"], ["78", "gi|285309967", "O04916", "CL2995.Contig22_All", "4.00", "", "5.01", "22.90", "", "22.40", "2", "", "4", "Aconitate hydratase", "Solanum tuberosum"], ["79", "gi|224119508", "Q9SYG7", "CL12585.Contig1_All", "2.76", "", "2.47", "11.80", "", "15.90", "3", "", "1", "Aldehyde dehydrogenase family 7 member B4", "Arabidopsis thaliana"], ["80", "gi|225438980", "O64816", "CL136.Contig4_All", "0.37", "", "1.44", "15.20", "", "27.50", "1", "", "1", "Casein kinase II subunit alpha", "Arabidopsis thaliana"], ["81", "gi|224056853", "P46256", "Unigene21704_All", "6.08", "", "5.67", "31.00", "", "36.80", "8", "", "10", "Fructose-bisphosphate aldolase", "Pisum sativum"], ["82", "gi|6563322", "O04266", "Unigene25085_All", "2.04", "", "2.00", "39.40", "", "37.30", "6", "", "6", "GTP-binding protein SAR1A", "Brassica campestris"], ["83", "gi|224113157", "O81832", "CL3993.Contig2_All", "2.01", "", "2.00", "12.80", "", "13.90", "2", "", "2", "G-type lectin S-receptor-like serine/threonine-protein kinase At4g27290", "Arabidopsis thaliana"], ["84", "gi|225435578", "Q39202", "CL16541.Contig3_All", "2.53", "", "2.29", "16.80", "", "17.30", "2", "", "2", "G-type lectin S-receptor-like serine/threonine-protein kinase RLK1", "Arabidopsis thaliana"], ["85", "gi|406870037", "P09189", "CL2270.Contig2_All", "2.78", "", "3.55", "76.20", "", "78.10", "5", "", "8", "Heat shock cognate 70 kDa protein", "Petunia hybrida"], ["86", "gi|1708314", "P51819", "CL1535.Contig1_All", "1.79", "", "5.80", "47.20", "", "41.60", "24", "", "29", "Heat shock protein 83", "Ipomoea nil"], ["87", "gi|359493983", "C0LGN2", "Unigene56808_All", "5.42", "", "2.00", "18.20", "", "19.20", "3", "", "1", "Leucine-rich repeat receptor-like serine/threonine-protein kinase At3g14840", "Arabidopsis thaliana"], ["88", "gi|225447810", "C0LGH2", "CL11120.Contig8_All", "2.53", "", "2.00", "24.50", "", "25.20", "1", "", "1", "LRR receptor-like serine/threonine-protein kinase At1g56130", "Arabidopsis thaliana"], ["89", "gi|255571730", "C0LGT6", "CL11164.Contig3_All", "0.92", "", "6.30", "26.80", "", "23.60", "1", "", "3", "LRR receptor-like serine/threonine-protein kinase EFR", "Arabidopsis thaliana"], ["90", "gi|255546773", "P98204", "CL587.Contig1_All", "2.00", "", "0.48", "12.80", "", "18.50", "1", "", "1", "Phospholipid-transporting ATPase 1", "Arabidopsis thaliana"], ["91", "gi|224095202", "Q9C660", "Unigene8986_All", "2.00", "", "2.00", "18.90", "", "23.00", "1", "", "1", "Proline-rich receptor-like protein kinase PERK10", "Arabidopsis thaliana"], ["92", "gi|356526137", "Q9LK03", "CL14215.Contig2_All", "2.00", "", "2.00", "26.50", "", "20.00", "1", "", "1", "Proline-rich receptor-like protein kinase PERK2", "Arabidopsis thaliana"], ["93", "gi|302783030", "Q67UF5", "CL3927.Contig4_All", "3.39", "", "2.00", "27.70", "", "28.40", "3", "", "4", "Protein disulfide isomerase-like 2–3", "Oryza sativa subsp. japonica"], ["94", "gi|296088320", "Q35638", "Unigene54779_All", "1.52", "", "1.17", "29.00", "", "21.40", "1", "", "1", "Rac-like GTP-binding protein RHO1", "Pisum sativum"], ["95", "gi|359479658", "", "CL6981.Contig1_All", "2.51", "", "4.04", "23.10", "", "20.90", "2", "", "2", "Serine/threonine-protein kinase BUD32 homolog", "Vitis vinifera"], ["96", "gi|386870491", "P11796", "Unigene31392_All", "4.00", "", "6.00", "48.70", "", "37.60", "3", "", "5", "Superoxide dismutase [Mn]", "Nicotiana plumbaginifolia"], ["97", "gi|359496003", "", "CL13681.Contig2_All", "1.00", "", "1.40", "7.00", "", "24.70", "1", "", "1", "Transaldolase-like", "Vitis vinifera"], ["98", "gi|224113019", "O82702", "Unigene35531_All", "1.55", "", "2.09", "67.50", "", "48.10", "12", "", "9", "V-type proton ATPase subunit G 1", "Nicotiana tabacum"], ["99", "gi|44917147", "O49996", "Unigene34923_All", "", "2.00", "6.00", "", "45.20", "62.10", "", "3", "10", "14-3-3-like protein D", "Nicotiana tabacum"], ["100", "gi|225465653", "", "CL3375.Contig1_All", "", "1.80", "1.22", "", "30.60", "9.60", "", "1", "1", "26S proteasome non-ATPase regulatory subunit 1", "Vitis vinifera"], ["101", "gi|225451255", "", "Unigene49648_All", "", "2.02", "4.00", "", "23.30", "52.40", "", "1", "2", "26S proteasome non-ATPase regulatory subunit 11 isoform 2", "Vitis vinifera"], ["102", "gi|225427157", "Q8LPK2", "CL12866.Contig4_All", "", "2.92", "2.01", "", "12.80", "19.40", "", "2", "1", "ABC transporter B family member 2", "Arabidopsis thaliana"], ["103", "gi|296085461", "Q8LPJ4", "CL6385.Contig3_All", "", "2.93", "6.88", "", "15.00", "22.90", "", "4", "4", "ABC transporter E family member 2", "Arabidopsis thaliana"], ["104", "gi|2493046", "Q40089", "CL7437.Contig3_All", "", "10.51", "7.86", "", "56.90", "53.40", "", "9", "7", "ATP synthase subunit delta'", "Ipomoea batatas"], ["105", "gi|267631890", "P28582", "Unigene22237_All", "", "2.88", "8.71", "", "28.90", "28.90", "", "4", "6", "Calcium-dependent protein kinase", "Daucus carota"], ["106", "gi|11131745", "P93508", "Unigene55350_All", "", "0.54", "1.17", "", "18.30", "8.70", "", "1", "1", "Calreticulin", "Ricinus communis"], ["107", "gi|255566201", "", "CL6055.Contig2_All", "", "3.95", "3.92", "", "34.30", "40.70", "", "2", "2", "Co-chaperone protein HscB", "Ricinus communis"], ["108", "gi|225462922", "Q8W207", "CL6827.Contig1_All", "", "1.23", "2.00", "", "12.10", "23.20", "", "1", "2", "COP9 signalosome complex subunit 2", "Arabidopsis thaliana"], ["109", "gi|225430043", "Q08298", "CL6583.Contig2_All", "", "6.00", "4.00", "", "33.60", "15.20", "", "3", "4", "Dehydration-responsive protein RD22", "Arabidopsis thaliana"], ["110", "gi|359477103", "P22242", "Unigene33129_All", "", "8.04", "5.58", "", "19.70", "37.50", "", "4", "3", "Desiccation-related protein PCC13-62", "Craterostigma plantagineum"], ["111", "gi|224120498", "P21616", "CL3527.Contig4_All", "", "2.00", "4.00", "", "56.90", "55.60", "", "1", "2", "Pyrophosphate-energized vacuolar membrane proton pump", "Vigna radiata var. radiata"], ["112", "gi|255562954", "Q2MHE4", "Unigene13016_All", "", "3.03", "7.85", "", "13.30", "22.20", "", "1", "4", "Serine/threonine-protein kinase HT1", "Arabidopsis thaliana"], ["113", "gi|225580057", "Q9XIC7", "CL10222.Contig1_All", "", "1.66", "1.00", "", "16.50", "25.90", "", "1", "2", "Somatic embryogenesis receptor kinase 2", "Arabidopsis thaliana"], ["114", "gi|75326539", "Q75VR1", "CL1554.Contig12_All", "", "2.74", "1.33", "", "10.30", "15.30", "", "2", "1", "Two pore calcium channel protein 1A", "Nicotiana tabacum"], ["115", "gi|148907059", "Q9LHA4", "CL3237.Contig1_All", "", "7.19", "1.74", "", "20.50", "25.90", "", "6", "4", "V-type proton ATPase subunit d2", "Arabidopsis thaliana"]], "row_count": 117, "column_count": 15, "numeric_cells": 1347, "header_rows": 2, "locator": "section[5]/table-wrap[2]#pone.0133386.t002"}}], "gaps": ["asset:data:geo:PXD000771 not downloaded", "asset:data:geo:PXD000771 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "False discovery rate (FDR)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Identified proteins for each biological replicate were selected based on a false discovery rate (FDR) of < 1%."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (False discovery rate (FDR)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD000771"], "resolved_accessions": ["PXD000771"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000771."], "basis": "The paper names PXD000771 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26193361", "data:geo:PXD000771", "asset:table:pmid:26193361:1", "asset:table:pmid:26193361:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD000771"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:13Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 76637, "completion_tokens": 2781, "cached_tokens": 1544}}, "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:26193361", "type": "paper", "label": "pmid:26193361"}, {"id": "source:pmid:26193361", "type": "manuscript", "label": "PMID 26193361 full text"}, {"id": "data:geo:PXD000771", "type": "dataset", "label": "GEO PXD000771"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26193361", "type": "paper", "label": "pmid:26193361"}, {"id": "source:pmid:26193361", "type": "manuscript", "label": "PMID 26193361 full text"}, {"id": "data:geo:PXD000771", "type": "dataset", "label": "GEO PXD000771"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26193361", "type": "extraction", "used": ["source:pmid:26193361"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD000771", "type": "accession_resolution", "used": ["data:geo:PXD000771"], "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:26193361", "parent_hash": "sha256:e9d897ce92615a7c0cf132dbb57d04d808cd9fc405f96ce0702699313bfc4124", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD000771 licence not read", "asset:data:geo:PXD000771 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": ["Proteomic Characterisation of the Salt Gland-Enriched", "s. This paper reports for the first time the proteomic analysis of salt gland-enriched tissues of a", "n mechanisms in salt glands, we used shotgun proteomics to compare the protein profiles of salt glan", "ounds in the samples. Sample preparation and LC-MS/MS analysis Each sample (300μg) was reduced by"], "order_basis": "paper_text_order:0", "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":"2026-11-04T02:48:39+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}}}