{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:23462205", "kind": "science-record", "revision": 8, "content_hash": "sha256:b1b7fda7209248e8c5c02c27fa104f419d6911243b0edd5569ec9f0904f00e53", "created_at": "2026-11-01T15:40:02Z", "updated_at": "2026-11-01T22:41:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis.", "doi": "10.1074/mcp.M112.025635", "pmid": "23462205", "authors": ["Lisa M Wolfe", "Usha Veeraraghavan", "Susan Idicula-Thomas", "Stephan Schürer", "Krister Wennerberg", "Robert Reynolds", "Gurdyal S Besra", "Karen M Dobos"], "journal": "Molecular & cellular proteomics : MCP", "year": 2013, "abstract": "Tuberculosis, caused by Mycobacterium tuberculosis, remains one of the leading causes of death worldwide despite extensive research, directly observed therapy using multidrug regimens, and the widespread use of a vaccine. The majority of patients harbor the bacterium in a state of metabolic dormancy. New drugs with novel modes of action are needed to target essential metabolic pathways in M. tuberculosis; ATP-competitive enzyme inhibitors are one such class. Previous screening efforts for ATP-competitive enzyme inhibitors identified several classes of lead compounds that demonstrated potent anti-mycobacterial efficacy as well as tolerable levels of toxicity in cell culture. In this report, a probe-based chemoproteomic approach was used to selectively profile the M. tuberculosis ATP-binding proteome in normally growing and hypoxic M. tuberculosis. From these studies, 122 ATP-binding proteins were identified in either metabolic state, and roughly 60% of these are reported to be essential for survival in vitro. These data are available through ProteomeXchange with identifier PXD000141. Protein families vital to the survival of the tubercle bacillus during hypoxia emerged from our studies. Specifically, along with members of the DosR regulon, several proteins involved in energy metabolism (Icl/Rv0468 and Mdh/Rv1240) and lipid biosynthesis (UmaA/Rv0469, DesA1/Rv0824c, and DesA2/Rv1094) were found to be differentially abundant in hypoxic versus normal growing cultures. These pathways represent a subset of proteins that may be relevant therapeutic targets for development of novel ATP-competitive antibiotics.", "claims": [{"id": "claim-method", "statement": "Statistical analysis was performed using Fisher's exact test in the comparison of two groups (i.e. normal-ATP versus hypoxic-ATP or normal-ATP versus normal-ATPγS).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23462205", "locator": "sections[12] \"Statistical Analysis\" paragraph 2", "quote": "Statistical analysis was performed using Fisher's exact test in the comparison of two groups (i.e. normal-ATP versus hypoxic-ATP or normal-ATP versus normal-ATPγS)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository (16) with the dataset identifier PXD000141.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23462205", "locator": "sections[11] \"Criteria for Protein Identification\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository (16) with the dataset identifier PXD000141."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 122 ATP-binding proteins in normally growing or hypoxic Mycobacterium tuberculosis, approximately 60% of which are essential for survival in vitro; the proteomics data are available through ProteomeXchange under identifier PXD000141.", "kind": "quantitative", "target": {"value": 60.0, "unit": "per cent", "tolerance": null, "source": "From these studies, 122 ATP-binding proteins were identified in either metabolic state, and roughly 60% of these are reported to be essential for survival in vitro. These data are available through ProteomeXchange with identifier PXD000141."}, "evidence": [{"asset": "source:pmid:23462205", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "From these studies, 122 ATP-binding proteins were identified in either metabolic state, and roughly 60% of these are reported to be essential for survival in vitro. These data are available through ProteomeXchange with identifier PXD000141."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 122 ATP-binding proteins in normally growing or hypoxic Mycobacterium tuberculosis, approximately 60% of which are essential for survival in vitro; the proteomics data are available through ProteomeXchange under identifier PXD000141.", "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:23462205"], "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:PXD000141"], "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:PXD000141"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:23462205", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1074/mcp.M112.025635", "sha256": "sha256:39122d70b18f1265050755a9ff96ef8f90e4dce8adc387733fb0fdd7c7867af8", "bytes": 62743, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1074/mcp.M112.025635", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC3675820", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD000141", "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=PXD000141", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000141", "version": null, "note": "The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository (16) with the dataset identifier PXD000141.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository (16) with the dataset identifier PXD000141.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Mycobacterium tuberculosis ATP-binding Proteome", "resolution_checked_at": "2026-10-31T18:28:21Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:23462205:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8e9a6c750b4cef584599f87c9cea27fcff9b7b2cdd871ccf637084664836122b", "bytes": 3500, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[1]#TI", "version": null, "note": "Proteins with increased abundance during normal growth", "structure": {"pmcid": "PMC3675820", "section_index": 22, "section_title": "Differential Abundance of Proteins in Normoxic (Normal) Versus Hypoxic State Bacteria", "row_count": 39, "column_count": 7}, "table": {"label": "Table I", "caption": "Proteins with increased abundance during normal growth", "rows": [["Identified proteins", "Accession no.", "Molecular mass", "Fisher's exact test (p value)", "Normal NSAF", "Hypoxic NSAFa", "Log fold change"], ["Polyphosphate kinase, Ppk", "Rv2984", "83 kDa", "(0.0000)", "66", "1", "6.04"], ["Phosphoglycerate kinase, Pgk", "Rv1437", "43 kDa", "(0.0000)", "57", "2", "4.83"], ["Acyl-CoA dehydrogenase, FadE4", "Rv0231", "63 kDa", "(0.0002)", "23", "1", "4.52"], ["Dehydrogenase", "Rv3389c", "30 kDa", "(0.0010)", "19", "1", "4.25"], ["19-kDa lipoprotein antigen precursor, LpqH", "Rv3763", "15 kDa", "(0.0021)", "17", "1", "4.09"], ["Immunogenic protein, Mpt64", "Rv1980c", "25 kDa", "(0.0021)", "17", "1", "4.09"], ["Hypothetical protein", "Rv2319c", "32 kDa", "(0.0021)", "17", "1", "4.09"], ["Aminomethyltransferase, GcvT", "Rv2211c", "40 kDa", "(0.0021)", "17", "1", "4.09"], ["Superoxide dismutase soda", "Rv3846", "23 kDa", "(0.0031)", "16", "1", "4.00"], ["Cysteinyl-tRNA synthetase 1, CysS1", "Rv3580c", "52 kDa", "(0.0031)", "16", "1", "4.00"], ["DNA polymerase I, PolA", "Rv1629", "98 kDa", "(0.0031)", "16", "1", "4.00"], ["Transmembrane serine/threonine-protein kinase E, PknE", "Rv1743", "61 kDa", "(0.0031)", "16", "1", "4.00"], ["Iron-regulated short-chain dehydrogenase/reductase", "Rv3224", "30 kDa", "(0.0006)", "26", "2", "3.70"], ["Fatty-acid-CoA ligase, FadD23", "Rv3826", "63 kDa", "(0.0099)", "13", "1", "3.70"], ["Leucyl-tRNA synthetase, LeuS", "Rv0041", "108 kDa", "(0.0150)", "12", "1", "3.58"], ["Pyridoxamine 5-phosphate oxidase, PdxH", "Rv2607", "25 kDa", "(0.0150)", "12", "1", "3.58"], ["Conserved hypothetical protein", "Rv2624c", "29 kDa", "(0.0002)", "34", "3", "3.50"], ["Aldehyde dehydrogenase", "Rv0458", "55 kDa", "(0.0066)", "19", "2", "3.25"], ["Acetyl-/propionyl-CoA carboxylase α subunit, AccA1", "Rv2501c", "71 kDa", "(0.0001)", "45", "5", "3.17"], ["Fatty-acid-CoA ligase, FadD7", "Rv0119", "55 kDa", "(0.0020)", "27", "3", "3.17"], ["Electron transfer flavoprotein β subunit, FixA", "Rv3029c", "28 kDa", "(0.0020)", "27", "3", "3.17"], ["Fatty-acid-CoA ligase, FadD36", "Rv1193", "50 kDa", "(0.0460)", "9", "1", "3.17"], ["Transferase", "Rv1201c", "33 kDa", "(0.0460)", "9", "1", "3.17"], ["Phosphoribosylamine-glycine ligase, PurD", "Rv0772", "44 kDa", "(0.0028)", "26", "3", "3.12"], ["Pyruvate kinase, PykA", "Rv1617", "51 kDa", "(0.0021)", "31", "4", "2.95"], ["Low molecular weight protein antigen, Cfp2", "Rv2376c", "17 kDa", "(0.0250)", "15", "2", "2.91"], ["Glutamyl-tRNA", "Rv3009c", "55 kDa", "(0.0000)", "83", "12", "2.79"], ["Transmembrane serine/threonine-protein kinase H, PknH", "Rv1266c", "67 kDa", "(0.0036)", "33", "5", "2.72"], ["Conserved alanine-rich protein", "Rv2744c", "29 kDa", "(0.0480)", "13", "2", "2.70"], ["Transmembrane serine/threonine-protein kinase D, PknD", "Rv0931c", "70 kDa", "(0.0005)", "51", "8", "2.67"], ["Conserved hypothetical protein", "Rv2159c", "36 kDa", "(0.0320)", "18", "3", "2.58"], ["ATP-dependent protease ATP-binding subunit, ClpC1", "Rv3596c", "94 kDa", "(0.0000)", "181", "32", "2.50"], ["Glutamine synthetase, GlnA2", "Rv2222c", "50 kDa", "(0.0280)", "22", "4", "2.46"], ["30 S ribosomal protein S1, RpsA", "Rv1630", "53 kDa", "(0.0360)", "21", "4", "2.39"], ["Succinyl-CoA synthetase β chain, SucC", "Rv0951", "41 kDa", "(0.0170)", "40", "9", "2.15"], ["Endopeptidase ATP-binding protein chain B, ClpB", "Rv0384c", "93 kDa", "(0.0003)", "131", "33", "1.99"], ["Glutamine synthetase, GlnA1", "Rv2220", "54 kDa", "(0.0200)", "65", "18", "1.85"], ["10-kDa chaperonin, GroES", "Rv3418c", "11 kDa", "(0.0049)", "136", "41", "1.73"]], "row_count": 39, "column_count": 7, "numeric_cells": 236, "header_rows": 1, "locator": "section[22]/table-wrap[1]#TI"}}, {"id": "asset:table:pmid:23462205:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ad734e78526b48173d39fa0e8c82935ee62b48033a6dfed1a952725d6e6f9cea", "bytes": 2319, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[2]#TII", "version": null, "note": "Proteins with increased abundance during hypoxic growth", "structure": {"pmcid": "PMC3675820", "section_index": 22, "section_title": "Differential Abundance of Proteins in Normoxic (Normal) Versus Hypoxic State Bacteria", "row_count": 23, "column_count": 7}, "table": {"label": "Table II", "caption": "Proteins with increased abundance during hypoxic growth", "rows": [["Identified proteins", "Accession no.", "Molecular mass", "Fisher's exact test (p value)", "Normal NSAa", "Hypoxic NSAF", "Log fold change"], ["Conserved hypothetical protein", "Rv2623", "32 kDa", "(0.0000)", "1", "14", "−3.81"], ["Acyl-(acyl-carrier protein) desaturase, DesA1", "Rv0824c", "39 kDa", "(0.0000)", "1", "12", "−3.58"], ["Hypothetical protein, Acg", "Rv2032", "37 kDa", "(0.0003)", "1", "8", "−3.00"], ["Phosphoribosylaminoimidazole-succinocarboxamide synthase, PurC", "Rv0780", "33 kDa", "(0.0010)", "1", "7", "−2.81"], ["Ketol-acid reductoisomerase, IlvC", "Rv3001c", "36 kDa", "(0.0010)", "1", "7", "−2.81"], ["Acyl-(acyl-carrier protein) desaturase DesA2", "Rv1094", "31 kDa", "(0.0000)", "2", "12", "−2.58"], ["Isocitrate lyase, Icl", "Rv0467", "47 kDa", "(0.0033)", "1", "6", "−2.58"], ["10-kDa culture filtrate antigen, EsxB", "Rv3874", "11 kDa", "(0.0100)", "1", "5", "−2.32"], ["40-kDa secreted l-alanine dehydrogenase, Ald", "Rv2780", "39 kDa", "(0.0000)", "29", "134", "−2.21"], ["Citrate synthase I, GltA2", "Rv0896", "48 kDa", "(0.0320)", "1", "4", "−2.00"], ["DNA gyrase subunit B, GyrB", "Rv0005", "78 kDa", "(0.0320)", "1", "4", "−2.00"], ["Transcription termination factor ρ", "Rv1297", "65 kDa", "(0.0000)", "4", "15", "−1.91"], ["Iron-regulated heparin-binding hemagglutinin, HbhA", "Rv0475", "22 kDa", "(0.0004)", "3", "11", "−1.87"], ["ATP synthase α chain, AtpA", "Rv1308", "59 kDa", "(0.0011)", "4", "11", "−1.46"], ["Macrolide-transport ATP-binding protein ABC transporter", "Rv2477c", "62 kDa", "(0.0005)", "5", "13", "−1.38"], ["6-Phosphofructokinase, PfkA", "Rv3010c", "37 kDa", "(0.0140)", "5", "9", "-0.85"], ["Fatty-acid oxidation protein, FadB", "Rv0860", "76 kDa", "(0.0010)", "10", "17", "−0.77"], ["Heat shock protein, HspX", "Rv2031c", "16 kDa", "(0.0000)", "133", "223", "−0.75"], ["Conserved hypothetical protein", "Rv1738", "11 kDa", "(0.0019)", "10", "16", "−0.68"], ["Bifunctional polyribonucleotide nucleotidyltransferase, GpsI", "Rv2783c", "80 kDa", "(0.0026)", "13", "18", "−0.47"], ["Adenosylhomocysteinase, SahH", "Rv3248c", "54 kDa", "(0.0000)", "45", "53", "−0.24"], ["Iron-regulated aconitate hydratase, Acn", "Rv1475c", "102 kDa", "(0.0490)", "10", "11", "−0.14"]], "row_count": 23, "column_count": 7, "numeric_cells": 135, "header_rows": 1, "locator": "section[22]/table-wrap[2]#TII"}}, {"id": "asset:table:pmid:23462205:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:90129f1fa03099ad985fb3d2171e1157be533c28ffacab7fac909d9e4d0a4534", "bytes": 3517, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[1]#TIII", "version": null, "note": "Competitive and transient binders of desthiobiotin-ATP in hypoxic cultures", "structure": {"pmcid": "PMC3675820", "section_index": 23, "section_title": "ATP Binding Properties of the M. tuberculosis ATPome", "row_count": 37, "column_count": 7}, "table": {"label": "Table III", "caption": "Competitive and transient binders of desthiobiotin-ATP in hypoxic cultures", "rows": [["", "Gene no.", "Molecular mass", "p value", "Avg. NSAF_ATPγSa", "Avg. NSAF_ATPb", "-Fold change"], ["Competitive binders of desthiobiotin-ATP"], ["Fatty-acid oxidation protein, FadB", "Rv0860", "76 kDa", "(0.0039)", "1", "6.33", "6.33"], ["Inosine-5-monophosphate dehydrogenase, GuaB3", "Rv3410c", "39 kDa", "(0.0056)", "1", "6.00", "6.00"], ["Transcription termination factor ρ", "Rv1297", "65 kDa", "(0.0079)", "1", "5.67", "5.67"], ["Macrolide-transport ATP-binding protein, ABC transporter", "Rv2477c", "62 kDa", "(0.0160)", "1", "5.00", "5.00"], ["Endopeptidase ATP-binding protein chain B, ClpB", "Rv0384c", "93 kDa", "(0.0031)", "2.5", "11.67", "4.67"], ["Iron-regulated heparin-binding hemagglutinin, HbhA", "Rv0475", "22 kDa", "(0.0320)", "1", "4.33", "4.33"], ["Adenosylhomocysteinase, SahH", "Rv3248c", "54 kDa", "(0.0065)", "5.5", "18.33", "3.33"], ["Chaperone protein, DnaK", "Rv0350", "67 kDa", "(0.0001)", "16", "50.00", "3.13"], ["Adenylate kinase, Adk", "Rv0733", "20 kDa", "(0.0400)", "8", "20.33", "2.54"], ["Acyl-(acyl-carrier protein) desaturase, DesA1c", "Rv0824c", "39 kDa", "(0.2200)", "2", "4.67", "2.33"], ["ATP synthase β chain, AtpDc", "Rv1310", "53 kDa", "(0.1500)", "5", "11.33", "2.27"], ["Bifunctional acetyl-/propionyl-coenzyme A carboxylase α chain, AccA3c", "Rv3285", "64 kDa", "(0.2600)", "3", "6.33", "2.11"], ["Transient binders of desthiobiotn-ATP", ""], ["50 S ribosomal protein L7/L12, RplL", "Rv0652", "13 kDa", "(0.3100)", "4.5", "8.67", "1.93"], ["10-kDa chaperonin, GroES", "Rv3418c", "11 kDa", "(0.3600)", "8", "14.33", "1.79"], ["ATP-dependent protease ATP-binding subunit, ClpC1", "Rv3596c", "94 kDa", "(0.5000)", "7", "11.33", "1.62"], ["60-kDa chaperonin 1, GroEL1", "Rv3417c", "56 kDa", "(0.5100)", "3.5", "5.67", "1.62"], ["Conserved hypothetical protein", "Rv2623", "32 kDa", "(0.5600)", "3.5", "5.33", "1.52"], ["40-kDa secreted l-alanine dehydrogenase, Ald", "Rv2780", "39 kDa", "(0.0520)", "36", "45.33", "1.26"], ["Cold shock protein A, CspA", "Rv3648c", "7 kDa", "(0.4400)", "4", "5.00", "1.25"], ["60-kDa chaperonin 2, GroEL2", "Rv0440", "57 kDa", "(0.0000)", "135", "168.67", "1.25"], ["Heat shock protein, HspX", "Rv2031c", "16 kDa", "(0.0002)", "67.5", "75.00", "1.11"], ["Transmembrane serine/threonine-protein kinase A, PknA", "Rv0015c", "46 kDa", "(0.3100)", "4", "4.33", "1.08"], ["Isocitrate lyase, Icl", "Rv0467", "47 kDa", "(0.4300)", "2.5", "2.67", "1.07"], ["Integration host factor, MihF", "Rv1388", "21 kDa", "(0.0280)", "19", "20.00", "1.05"], ["6-Phosphofructokinase, PfkA", "Rv3010c", "37 kDa", "(0.3200)", "3.5", "3.67", "1.05"], ["Bifunctional polyribonucleotide nucleotidyltransferase, GpsI", "Rv2783c", "80 kDa", "(0.1600)", "6.5", "6.67", "1.03"], ["Iron-regulated elongation factor tu tuf", "Rv0685", "44 kDa", "(0.0120)", "20.5", "20.33", "0.99"], ["Propionyl-CoA carboxylase β chain 5, AccD5", "Rv3280", "59 kDa", "(0.5000)", "1.5", "1.33", "0.89"], ["Conserved hypothetical protein", "Rv3269", "10 kDa", "(0.1600)", "4.5", "4.00", "0.89"], ["Electron transfer flavoprotein β subunit, FixA", "Rv3029c", "28 kDa", "(0.3300)", "2", "1.67", "0.83"], ["Conserved hypothetical protein", "Rv1738", "11 kDa", "(0.0390)", "7.5", "6.00", "0.80"], ["Iron-regulated conserved hypothetical protein", "Rv1636", "15 kDa", "(0.0093)", "10", "7.33", "0.73"], ["Transmembrane serine/threonine-protein kinase D, PknD", "Rv0931c", "70 kDa", "(0.0100)", "6", "3.33", "0.56"], ["Conserved hypothetical protein", "Rv3127", "39 kDa", "(0.0640)", "3", "1.67", "0.56"]], "row_count": 37, "column_count": 7, "numeric_cells": 212, "header_rows": 1, "locator": "section[23]/table-wrap[1]#TIII"}}, {"id": "asset:table:pmid:23462205:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3332bd36f3a2aeddeb695e8f72648fb43d8dd0649e1d25f3513888ed645f80f7", "bytes": 9305, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[2]#TIV", "version": null, "note": "Competitive and transient binders of desthiobiotin-ATP in normal cultures", "structure": {"pmcid": "PMC3675820", "section_index": 23, "section_title": "ATP Binding Properties of the M. tuberculosis ATPome", "row_count": 101, "column_count": 7}, "table": {"label": "Table IV", "caption": "Competitive and transient binders of desthiobiotin-ATP in normal cultures", "rows": [["", "Gene no.", "Molecular mass", "p value", "Avg. NSAF_ATPγSa", "Avg. NSAF_ATPb", "Fold change"], ["Competitive Binders of Desthiobiotin-ATP", "", "", "", "", "", ""], ["Acetyl-/propionyl-CoA carboxylase α subunit, AccA1", "Rv2501c", "71 kDa", "(0.0000)", "1.00", "15.67", "15.67"], ["Glutamyl-tRNA amidotransferase subunit B, GatB", "Rv3009c", "55 kDa", "(0.0000)", "2.33", "28.33", "12.14"], ["Inosine-5-monophosphate dehydrogenase, GuaB3", "Rv3410c", "39 kDa", "(0.0000)", "1.00", "11.67", "11.67"], ["Transmembrane serine/threonine-protein kinase H, PknH", "Rv1266c", "67 kDa", "(0.0000)", "1.00", "11.33", "11.33"], ["Fatty-acid-CoA ligase, FadD7", "Rv0119", "55 kDa", "(0.0000)", "1.00", "9.67", "9.67"], ["Phosphoribosylamine-glycine ligase, PurD", "Rv0772", "44 kDa", "(0.0000)", "1.00", "9.33", "9.33"], ["Tryptophanyl-tRNA synthetase, TrpS", "Rv3336c", "36 kDa", "(0.0001)", "1.00", "7.00", "7.00"], ["Polyphosphate kinase, Ppk", "Rv2984", "83 kDa", "(0.0000)", "3.33", "22.67", "6.80"], ["Phosphoglycerate kinase, Pgk", "Rv1437", "43 kDa", "(0.0000)", "3.00", "19.67", "6.56"], ["Cysteinyl-tRNA synthetase 1, CysS1", "Rv3580c", "52 kDa", "(0.0005)", "1.00", "5.67", "5.67"], ["Fatty-acid-CoA ligase, FadD23", "Rv3826", "63 kDa", "(0.0014)", "1.00", "5.00", "5.00"], ["Universal stress protein", "Rv2319c", "32 kDa", "(0.0012)", "1.33", "6.33", "4.75"], ["CTP synthase, PyrG", "Rv1699", "64 kDa", "(0.0024)", "1.00", "4.67", "4.67"], ["Phosphofructokinase, PfkB", "Rv2029c", "35 kDa", "(0.0073)", "1.00", "4.00", "4.00"], ["ATP-dependent protease ATP-binding subunit, ClpC1", "Rv3596c", "94 kDa", "(0.0000)", "15.33", "61.00", "3.98"], ["Anchored-membrane serine/threonine-protein kinase, PknF", "Rv1746", "51 kDa", "(0.0130)", "1.00", "3.67", "3.67"], ["Chaperone protein, HtpG", "Rv2299c", "73 kDa", "(0.0130)", "1.00", "3.67", "3.67"], ["DNA polymerase I, PolA", "Rv1629", "98 kDa", "(0.0078)", "1.67", "6.00", "3.60"], ["Acetate kinase, AckA", "Rv0409", "41 kDa", "(0.0220)", "1.00", "3.33", "3.33"], ["UDP-N-acetylmuramoylalanyl-d-glutamyl-2,6-diaminopimelate-d-alanyl-d-alanyl ligase, MurF", "Rv2157c", "52 kDa", "(0.0220)", "1.00", "3.33", "3.33"], ["Conserved hypothetical protein", "Rv3282", "23 kDa", "(0.0220)", "1.00", "3.33", "3.33"], ["Conserved hypothetical protein", "Rv2510c", "57 kDa", "(0.0220)", "1.00", "3.33", "3.33"], ["Fatty-acid-CoA ligase, FadD28", "Rv2941", "63 kDa", "(0.0077)", "2.33", "7.67", "3.29"], ["Nucleoside diphosphate kinase, NdkA", "Rv2445c", "15 kDa", "(0.0150)", "2.00", "6.33", "3.17"], ["40-kDa secreted l-alanine dehydrogenase, Ald", "Rv2780", "39 kDa", "(0.0066)", "3.00", "9.33", "3.11"], ["Adenosylhomocysteinase, SahH", "Rv3248c", "54 kDa", "(0.0017)", "5.00", "15.00", "3.00"], ["Pyruvate kinase, PykA", "Rv1617", "51 kDa", "(0.0053)", "3.67", "11.00", "3.00"], ["Malate synthase G, GlcB", "Rv1837c", "80 kDa", "(0.0420)", "1.67", "4.67", "2.80"], ["Aldehyde dehydrogenase", "Rv0458", "55 kDa", "(0.0350)", "2.67", "7.00", "2.63"], ["Adenylate kinase, Adk", "Rv0733", "20 kDa", "(0.0035)", "17.33", "36.67", "2.12"], ["transmembrane serine/threonine-protein kinase D, PknD", "Rv0931c", "70 kDa", "(0.0400)", "8.67", "17.67", "2.04"], ["ATP synthase β chain, AtpD", "Rv1310", "53 kDa", "(0.0250)", "13.33", "26.33", "1.98"], ["Transient binders of desthiobiotin-ATP"], ["Endopeptidase ATP-binding protein chain B, ClpB", "Rv0384c", "93 kDa", "(0.0410)", "25.33", "44.33", "1.75"], ["3-Hydroxyacyl-thioester dehydrogenase, HtdY", "Rv3389c", "30 kDa", "(0.4000)", "4.67", "7.00", "1.50"], ["Iron-regulated short-chain dehydrogenase/reductase", "Rv3224", "30 kDa", "(0.4100)", "6.33", "9.33", "1.47"], ["Aminomethyltransferase, GcvT", "Rv2211c", "40 kDa", "(0.4300)", "4.33", "6.33", "1.46"], ["Phosphopantetheine adenylyltransferase, KdtB", "Rv2965c", "18 kDa", "(0.4700)", "2.33", "3.33", "1.43"], ["Chaperone protein, DnaK", "Rv0350", "67 kDa", "(0.3800)", "40.00", "57.00", "1.43"], ["Cold shock protein A, CspA", "Rv3648c", "7 kDa", "(0.5300)", "5.67", "7.67", "1.35"], ["Secreted fibronectin-binding protein antigen", "85-B fbpB", "Rv1886c", "35 kDa", "(0.5400)", "2.00", "2.67"], ["Iron-regulated peptidyl-prolyl cis-trans isomerase, PpiA", "Rv0009", "19 kDa", "(0.5400)", "3.00", "4.00", "1.33"], ["Glutamine synthetase, GlnA2", "Rv2222c", "50 kDa", "(0.5500)", "6.00", "8.00", "1.33"], ["Pyruvate dehydrogenase E2 component, SucB", "Rv2215", "57 kDa", "(0.5500)", "7.33", "9.67", "1.32"], ["Acyl-CoA dehydrogenase, FadE5", "Rv0244c", "66 kDa", "(0.5700)", "3.33", "4.33", "1.30"], ["Pyruvate dehydrogenase E1 component, AceE", "Rv2241", "100 kDa", "(0.5700)", "4.67", "6.00", "1.29"], ["60-kDa chaperonin 2, GroEL2", "Rv0440", "57 kDa", "(0.0180)", "279.00", "352.00", "1.26"], ["Iron-regulated conserved hypothetical protein", "Rv1636", "15 kDa", "(0.3500)", "17.00", "21.00", "1.24"], ["Propionyl-CoA carboxylase β chain 5, AccD5", "Rv3280", "59 kDa", "(0.5800)", "3.00", "3.67", "1.22"], ["Low molecular weight protein antigen, Cfp2", "Rv2376c", "17 kDa", "(0.5000)", "4.67", "5.67", "1.21"], ["Glutamine synthetase, GlnA1", "Rv2220", "54 kDa", "(0.3000)", "17.67", "21.33", "1.21"], ["Heat shock protein, HspX", "Rv2031c", "16 kDa", "(0.1800)", "36.00", "43.33", "1.20"], ["Succinyl-CoA synthetase β chain, SucC", "Rv0951", "41 kDa", "(0.3500)", "11.67", "14.00", "1.20"], ["Oligoribonuclease, Orn", "Rv2511", "23 kDa", "(0.4800)", "5.00", "6.00", "1.20"], ["Protein transport protei, SecE2", "Rv0379", "8 kDa", "(0.5400)", "3.33", "4.00", "1.20"], ["l-Lactate dehydrogenase, LldD2", "Rv1872c", "45 kDa", "(0.4500)", "5.33", "6.33", "1.19"], ["Conserved hypothetical protein", "Rv2159c", "36 kDa", "(0.4300)", "5.67", "6.67", "1.18"], ["Bifunctional coenzyme A carboxylase α chain, AccA3", "Rv3285", "64 kDa", "(0.2800)", "13.67", "16.00", "1.17"], ["50 S ribosomal protein L7/L12, RplL", "Rv0652", "13 kDa", "(0.2500)", "16.00", "18.67", "1.17"], ["Conserved hypothetical protein", "Rv3269", "10 kDa", "(0.4800)", "4.00", "4.67", "1.17"], ["Ribosome recycling factor, Frr", "Rv2882c", "21 kDa", "(0.5700)", "2.33", "2.67", "1.14"], ["Superoxide dismutase, SodA", "Rv3846", "23 kDa", "(0.3900)", "5.33", "6.00", "1.13"], ["Transmembrane serine/threonine-protein kinase E, PknE", "Rv1743", "61 kDa", "(0.3900)", "5.33", "6.00", "1.13"], ["Two-component system transcriptional regulator, DevR", "Rv3133c", "23 kDa", "(0.4600)", "3.33", "3.67", "1.10"], ["Tetrahydrodipicolinate N-succinyltransferase", "Rv1201c", "33 kDa", "(0.4600)", "3.33", "3.67", "1.10"], ["Leucyl-tRNA synthetase, LeuS", "Rv0041", "108 kDa", "(0.3800)", "4.33", "4.67", "1.08"], ["Iron-regulated elongation factor tu tuf", "Rv0685", "44 kDa", "(0.0300)", "40.33", "43.33", "1.07"], ["Immunogenic protein, Mpt64", "Rv1980c", "25 kDa", "(0.3000)", "6.00", "6.33", "1.06"], ["30 S ribosomal protein S1, RpsA", "Rv1630", "53 kDa", "(0.2500)", "7.33", "7.67", "1.05"], ["Transmembrane serine/threonine-protein kinase A, PknA", "Rv0015c", "46 kDa", "(0.2100)", "8.67", "9.00", "1.04"], ["Transcriptional regulator", "Rv0023", "27 kDa", "(0.5600)", "1.67", "1.67", "1.00"], ["Hypothetical protein, Wag31", "Rv2145c", "28 kDa", "(0.4200)", "2.67", "2.67", "1.00"], ["Hypothetical protein", "Rv3818", "58 kDa", "(0.5000)", "2.00", "2.00", "1.00"], ["Conserved alanine-rich protein", "Rv2744c", "29 kDa", "(0.2800)", "5.00", "5.00", "1.00"], ["Enoyl-CoA hydratase, EchA9", "Rv1071c", "36 kDa", "(0.3900)", "3.00", "3.00", "1.00"], ["Conserved hypothetical protein", "Rv2140c", "19 kDa", "(0.5000)", "2.00", "2.00", "1.00"], ["Thiosulfate sulfurtransferase, CysA2", "Rv0815c", "31 kDa", "(0.5600)", "1.67", "1.67", "1.00"], ["Zinc-type alcohol dehydrogenase NAD-dependent, AdhB", "Rv0761c", "40 kDa", "(0.2300)", "4.67", "4.33", "0.93"], ["Transcriptional regulator, MoxR1", "Rv1479", "41 kDa", "(0.2800)", "3.33", "3.00", "0.90"], ["60-kDa chaperonin 1, GroEL1", "Rv3417c", "56 kDa", "(0.0270)", "16.33", "14.67", "0.90"], ["Meromycolate extension acyl carrier protein, AcpM", "Rv2244", "13 kDa", "(0.1400)", "6.33", "5.67", "0.89"], ["Haloalkane dehalogenase", "Rv2296", "33 kDa", "(0.1500)", "6.00", "5.33", "0.89"], ["Succinyl-CoA synthetase α chain, SucD", "Rv0952", "31 kDa", "(0.1600)", "5.67", "5.00", "0.88"], ["ATP synthase α chain, AtpA", "Rv1308", "59 kDa", "(0.3300)", "2.33", "2.00", "0.86"], ["Integration host factor, MihF", "Rv1388", "21 kDa", "(0.0001)", "41.33", "34.67", "0.84"], ["acyl-CoA dehydrogenase, FadE25", "Rv3274c", "42 kDa", "(0.3500)", "2.00", "1.67", "0.83"], ["DNA polymerase III β chain, DnaN", "Rv0002", "42 kDa", "(0.3500)", "2.00", "1.67", ""], ["Pyridoxamine 5-phosphate oxidase, PdxH", "Rv2607", "25 kDa", "(0.1100)", "5.67", "4.67", "0.82"], ["10-kDa chaperonin, GroES", "Rv3418c", "11 kDa", "(0.0000)", "50.33", "40.67", "0.81"], ["Iron-regulated aconitate hydratase, Acn", "Rv1475c", "102 kDa", "(0.1200)", "5.00", "4.00", "0.80"], ["30 S ribosomal protein S16, RpsP", "Rv2909c", "17 kDa", "(0.3800)", "1.67", "1.33", "0.80"], ["Hypothetical protein, Cfp17", "Rv1827", "17 kDa", "(0.2000)", "3.33", "2.67", "0.80"], ["Fructose-bisphosphate aldolase, Fba", "Rv0363c", "37 kDa", "(0.2000)", "3.00", "2.33", "0.78"], ["Short-chain type dehydrogenase/reductase", "Rv0148", "30 kDa", "(0.2000)", "3.00", "2.33", "0.78"], ["Transcriptional regulator, TetR family", "Rv0144", "31 kDa", "(0.2000)", "3.00", "2.33", "0.78"], ["19-kDa lipoprotein antigen precursor, LpqH", "Rv3763", "15 kDa", "(0.0250)", "8.67", "6.33", "0.73"], ["Conserved hypothetical protein", "Rv2406c", "15 kDa", "(0.2100)", "2.33", "1.67", "0.71"], ["Electron transfer flavoprotein β subunit, FixA", "Rv3029c", "28 kDa", "(0.0039)", "13.67", "9.67", "0.71"], ["Enolase, Eno", "Rv1023", "45 kDa", "(0.1300)", "3.33", "2.33", "0.70"]], "row_count": 101, "column_count": 7, "numeric_cells": 607, "header_rows": 1, "locator": "section[23]/table-wrap[2]#TIV"}}], "gaps": ["asset:data:geo:PXD000141 not downloaded", "asset:data:geo:PXD000141 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "contingency_analysis", "specific": "fisher_exact", "label": "Categorical (contingency table) analysis", "dsl_operations": ["contingency_table", "chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Statistical analysis was performed using Fisher's exact test in the comparison of two groups (i.e. normal-ATP versus hypoxic-ATP or normal-ATP versus normal-ATPγS)."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "chi_square_test", "expected_value": 60.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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": ["contingency_table", "chi_square_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: fisher_exact."}, "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": ["PXD000141"], "resolved_accessions": ["PXD000141"], "statements": ["The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository (16) with the dataset identifier PXD000141."], "basis": "The paper names PXD000141 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["contingency_table", "chi_square_test"], "assets": ["source:pmid:23462205", "data:geo:PXD000141", "asset:table:pmid:23462205:1", "asset:table:pmid:23462205:2", "asset:table:pmid:23462205:3", "asset:table:pmid:23462205:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD000141"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:19Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 125636, "completion_tokens": 2640, "cached_tokens": 94766}}, "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:23462205", "type": "paper", "label": "pmid:23462205"}, {"id": "source:pmid:23462205", "type": "manuscript", "label": "PMID 23462205 full text"}, {"id": "data:geo:PXD000141", "type": "dataset", "label": "GEO PXD000141"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:23462205", "type": "paper", "label": "pmid:23462205"}, {"id": "source:pmid:23462205", "type": "manuscript", "label": "PMID 23462205 full text"}, {"id": "data:geo:PXD000141", "type": "dataset", "label": "GEO PXD000141"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-23462205", "type": "extraction", "used": ["source:pmid:23462205"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD000141", "type": "accession_resolution", "used": ["data:geo:PXD000141"], "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:23462205", "parent_hash": "sha256:3a7f720637826e214c45510ad0ef415343c223bfa8890ce7a3f6368537ff4564", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD000141 licence not read", "asset:data:geo:PXD000141 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "contingency_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["contingency_table", "chi_square_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Statistical analysis was performed using Fisher's exact test in the comparison of two groups (i.e. normal-ATP versus hypoxic-ATP or normal-ATP versus normal-ATPγS)."], "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":"2026-11-04T02:46:43+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}}}