{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33758032", "kind": "science-record", "revision": 7, "content_hash": "sha256:27f134df596821282b855bddecc43e188ab93c73969a36353d7d0a5965a2c819", "created_at": "2026-11-01T15:41:30Z", "updated_at": "2026-11-01T22:03:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses.", "doi": "10.1128/mSystems.01305-20", "pmid": "33758032", "authors": ["Zhongyou Li", "Katja Koeppen", "Victoria I Holden", "Samuel L Neff", "Liviu Cengher", "Elora G Demers", "Dallas L Mould", "Bruce A Stanton", "Thomas H Hampton"], "journal": "mSystems", "year": 2021, "abstract": "The NCBI Gene Expression Omnibus (GEO) provides tools to query and download transcriptomic data. However, less than 4% of microbial experiments include the sample group annotations required to assess differential gene expression for high-throughput reanalysis, and data deposited after 2014 universally lack these annotations. Our algorithm GAUGE (general annotation using text/data group ensembles) automatically annotates GEO microbial data sets, including microarray and RNA sequencing studies, increasing the percentage of data sets amenable to analysis from 4% to 33%. Eighty-nine percent of GAUGE-annotated studies matched group assignments generated by human curators. To demonstrate how GAUGE annotation can lead to scientific insight, we created GAPE (GAUGE-annotated Pseudomonas aeruginosa and Escherichia coli transcriptomic compendia for reanalysis), a Shiny Web interface to analyze 73 GAUGE-annotated P. aeruginosa studies, three times more than previously available. GAPE analysis revealed that PA3923, a gene of unknown function, was frequently differentially expressed in more than 50% of studies and significantly coregulated with genes involved in biofilm formation. Follow-up wet-bench experiments demonstrate that PA3923 mutants are indeed defective in biofilm formation, consistent with predictions facilitated by GAUGE and GAPE. We anticipate that GAUGE and GAPE, which we have made freely available, will make publicly available microbial transcriptomic data easier to reuse and lead to new data-driven hypotheses.IMPORTANCE GEO archives transcriptomic data from over 5,800 microbial experiments and allows researchers to answer questions not directly addressed in published papers. However, less than 4% of the microbial data sets include the sample group annotations required for high-throughput reanalysis. This limitation blocks a considerable amount of microbial transcriptomic data from being reused easily. Here, we demonstrate that the GAUGE algorithm could make 33% of microbial data accessible to parallel mining and reanalysis. GAUGE annotations increase statistical power and, thereby, make consistent patterns of differential gene expression easier to identify. In addition, we developed GAPE (GAUGE-annotated Pseudomonas aeruginosa and Escherichia coli transcriptomic compendia for reanalysis), a Shiny Web interface that performs parallel analyses on P. aeruginosa and E. coli compendia. Source code for GAUGE and GAPE is freely available and can be repurposed to create compendia for other bacterial species.", "claims": [{"id": "claim-method", "statement": "The Mantel test assesses the correlation between the string distance matrix of sample titles and the Euclidean distance matrix of gene expression data (Fig. 1C).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33758032", "locator": "sections[3] \"GAUGE accurately selects and annotates sample groups, extending the number of studies that can be systematically analyzed.\" paragraph 2", "quote": "The Mantel test assesses the correlation between the string distance matrix of sample titles and the Euclidean distance matrix of gene expression data (Fig. 1C)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The source code of GAUGE and the P. aeruginosa and E. coli ANOVA compendia created in this study can be found at https://github.com/DartmouthStantonLab/GAUGE.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33758032", "locator": "sections[17] \"GAUGE and Shiny app availability.\" paragraph 2", "quote": "The source code of GAUGE and the P. aeruginosa and E. coli ANOVA compendia created in this study can be found at https://github.com/DartmouthStantonLab/GAUGE."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33758032"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33758032", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1128/mSystems.01305-20", "sha256": "sha256:2aa6f3e81e50792818ee0604297deafcc9a00f034cc3fde2d83ebae11ad4e40f", "bytes": 51168, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1128/mSystems.01305-20", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8547006", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:33758032:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6808fd62653bf4a31bd022fd5f03d759180fbebdfbb0ffcbcb7aecc9641dd03b", "bytes": 1000, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#tab1", "version": null, "note": "Top 10 most frequently differentially expressed genes in 73 GAUGE-annotated P. aeruginosa studies", "structure": {"pmcid": "PMC8547006", "section_index": 5, "section_title": "GAUGE-annotated ANOVA compendium reveals frequently differentially expressed genes with undefined functions.", "row_count": 11, "column_count": 5}, "table": {"label": "TABLE 1", "caption": "Top 10 most frequently differentially expressed genes in 73 GAUGE-annotated P. aeruginosa studies", "rows": [["Standing", "Locus tag", "Gene product description", "No. of studiesa", "Median log2 FCb"], ["1", "PA0105", "Cytochrome c oxidase, subunit II", "43", "2.882226"], ["2", "PA1041", "Probable outer membrane protein precursorc", "41", "2.765857"], ["3", "PA3723", "Probable FMN oxidoreductasec", "41", "2.654894"], ["4", "PA2851", "Translation elongation factor P", "41", "1.929715"], ["5", "PA2445", "Glycine cleavage system protein P2", "40", "3.101212"], ["6", "PA4296", "Two-component response regulator, PprB", "40", "3.019888"], ["7", "PA3418", "Leucine dehydrogenase", "40", "2.789049"], ["8", "PA5172", "Ornithine carbamoyltransferase, catabolic", "40", "2.625181"], ["9", "PA1984", "NAD+-dependent aldehyde dehydrogenase", "39", "3.385404"], ["10", "PA3923", "Hypothetical protein", "39", "2.942898"]], "row_count": 11, "column_count": 5, "numeric_cells": 40, "header_rows": 1, "locator": "section[5]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:33758032:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:40cda766f0a7b4cf73cca345a2f1fa8c3cd56e0512d4e3299176508746043555", "bytes": 1252, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#tab2", "version": null, "note": "GAPE identifies studies in which the biofilm formation pathway is enriched", "structure": {"pmcid": "PMC8547006", "section_index": 6, "section_title": "Correlation and pathway enrichment analysis suggest that hypothetical protein PA3923 plays a role in biofilm formation, a clinically relevant phenotype.", "row_count": 8, "column_count": 5}, "table": {"label": "TABLE 2", "caption": "GAPE identifies studies in which the biofilm formation pathway is enriched", "rows": [["GSE no.", "Titlea", "PA3923 DEb", "Biofilm formation pathway reportedc", "Reference"], ["GSE21966", "Transcriptional profiling of P. aeruginosa isolated from 3 individuals with cystic fibrosis over time", "", "✓", "32"], ["GSE62970", "Expression data of clinical P. aeruginosa isolates grown in vitro in minimal glucose medium", "✓", "", "NA"], ["GSE67006", "Expression data from P. aeruginosa wild type and Δanr grown as biofilms on ΔF508 cystic fibrosis bronchial epithelial cells (CFBEs)", "", "✓", "33"], ["GSE28719", "Gene expression of P. aeruginosa ΔPA1006/nbvF mutant in the absence and presence of nitrate", "✓", "✓", "34"], ["GSE39044", "Regulon of transcriptional regulator PA2449 in P. aeruginosa PAO1", "✓", "", "35"], ["GSE8408", "Transcriptomic analysis of the sulfate starvation 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To establish GAUGE, we used microarray studies because they have a standardized mat", "me is applied to Fig. 3 and 4. GAUGE selects microarray studies and detects sample groups with high", "P value distribution of 368 Mantel tests of microarray studies. (B and C) Annotation rate (B) and e"], "order_basis": "paper_text_order:550", "id": "assay:1"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d 96-well enzyme-linked immunosorbent assay (ELISA) plates or on bovine serum albumin (BSA)-coa", "on bovine serum albumin (BSA)-coated 96-well ELISA plates as a control (22). Biofilm formation", "the wild-type PA14 strain on laminin-coated ELISA plates and BSA-coated ELISA plates. Each dat", "n laminin-coated ELISA plates and BSA-coated ELISA plates. 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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":"2026-11-04T02:15:12+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}}}