{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40670404", "kind": "science-record", "revision": 4, "content_hash": "sha256:50f9c2bbf369ba61905714dfcf93eb87323ad44ea5ea66bfc2b3c8710aae9c17", "created_at": "2026-11-01T20:30:46Z", "updated_at": "2026-11-01T22:56:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Potential diagnostic and therapeutic gene in chronic low back pain through pyroptosis modulation: A silico study based on the dataset analysis.", "doi": "10.1038/s41598-025-06756-6", "pmid": "40670404", "authors": ["Jintao Guo", "Tao Sun"], "journal": "Scientific reports", "year": 2025, "abstract": "Chronic low back pain (cLBP ) is a common condition that affects the quality of life, can be caused by disc degeneration, facet arthropathy, myofascial pain, sacroiliac joint pain, spondyloarthropathies, and nociplastic pain etc. Research suggests that excessive pyroptosis may trigger cytokine release and harmful inflammation, leading to tissue damage and organ dysfunction, which could be a potential molecular mechanism underlying these conditions. Our aim in this research was to look into the effects of genes associated with pyroptosis in cLBP, with the goal of describing possible markers for diagnosis and targets for treatment. A comprehensive analysis of Differentially Expressed Genes (DEGs) was performed utilizing the GSE177034 datasets sourced from the Gene Expression Omnibus (GEO) repository. GSE177034 included 98 patients admitted to the hospital for treatment of low back pain, all of whom had peripheral blood extracted and sequenced. We identified 883 DEGs, including 397 upregulated and 486 downregulated genes, in cLBP. The WGCNA revealed 11 co-expression modules, with the blue module presenting the utmost positive connection to pyroptosis. The GO and KEGG analyses showed that DEGs associated with pyroptosis were substantially enriched in pathways like the NF-kappaB transcription factor activity and the MyD88-dependent signaling pathway of Toll-like receptors. Machine learning approaches identified five pyroptosis relate hub genes (AVIL, PADI4, ARHGAP24, ST3GAL6, and BICDL2) as potential biomarkers. The cLBP diagnostic column chart model was established, demonstrating the accuracy of hub genes as biomarkers. A hub mRNA-related interaction network was constructed to identify potential therapeutic drugs, followed by verification of hub gene expression levels to validate their role in cLBP. Moreover, the investigation into immune cell infiltration revealed substantial disparities in the presence of five distinct immune cell types between the chronic LBP and acute LBP cohorts. Specifically, activated effector memory CD8 T cells (R = - 0.5407, p-value < 0.001) ,and CD56bright natural killer cells (R = - 0.5438, p-value < 0.001) were all found to be significantly different. These findings suggest that immune involvement may play a role in the development of cLBP. This study identified diagnostic biomarkers and therapeutic targets for cLBP, offering promising avenues for improved diagnosis and treatment. The identification of specific biomarkers, including AVIL, PADI4, ARHGAP24, ST3GAL6, and BICDL2, enhances diagnostic precision by enabling the stratification of cLBP subtypes based on underlying pathophysiology.", "claims": [{"id": "claim-method", "statement": "Statistical analysis was performed using R software, version 4.1.2. The Spearman correlation test was selected to ascertain the correlation between two variables. Comparisons between the two groups were made with the Wilcoxon test. Comparisons between three or more groups were made with the Kruskal–Wallis test. A two-tailed p-value of < 0.05 was indicative of statistical significance. The ‘pROC’ R package was used to create ROC curves and determine AUC values for the feature genes, thus assessing their potential as diagnostic indicators24.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40670404", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "Statistical analysis was performed using R software, version 4.1.2."}, {"asset": "source:pmid:40670404", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "The Spearman correlation test was selected to ascertain the correlation between two variables."}, {"asset": "source:pmid:40670404", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "Comparisons between the two groups were made with the Wilcoxon test."}, {"asset": "source:pmid:40670404", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "Comparisons between three or more groups were made with the Kruskal–Wallis test."}, {"asset": "source:pmid:40670404", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "A two-tailed p-value of < 0.05 was indicative of statistical significance."}, {"asset": "source:pmid:40670404", "locator": "sections[8] \"Utilizing receiver operating characteristic curve analysis for evaluation\" paragraph 2", "quote": "The ‘pROC’ R package was used to create ROC curves and determine AUC values for the feature genes, thus assessing their potential as diagnostic indicators24."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset(GSE177034) employed in this study are available via the GEO database (GeneExpressionOmnibus, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE177034). Genes related to pyroptosis were sourced from earlier investigations(10.1038/nri3452, 10.1038/s41420-021-00451-x, 10.1016/j.jsb.2017.08.001, 10.1038/s41568-019-0123-y, 10.1038/s41419-019-1883-8, 10.1111/imr.12296).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40670404", "locator": "sections[29] \"Data availability\" paragraph 2", "quote": "The dataset(GSE177034) employed in this study are available via the GEO database (GeneExpressionOmnibus, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE177034). Genes related to pyroptosis were sourced from earlier investigations(10.1038/nri3452, 10.1038/s41420-021-00451-x, 10.1016/j.jsb.2017.08.001, 10.1038/s41568-019-0123-y, 10.1038/s41419-019-1883-8, 10.1111/imr.12296)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Machine learning screening identified five pyroptosis-related hub genes—AVIL, PADI4, ARHGAP24, ST3GAL6, and BICDL2—as potential diagnostic biomarkers for chronic low back pain.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40670404", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Machine learning approaches identified five pyroptosis relate hub genes (AVIL, PADI4, ARHGAP24, ST3GAL6, and BICDL2) as potential biomarkers."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Machine learning screening identified five pyroptosis-related hub genes—AVIL, PADI4, ARHGAP24, ST3GAL6, and BICDL2—as potential diagnostic biomarkers for chronic low back pain.", "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:40670404"], "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:GSE177034"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE177034"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40670404", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-06756-6", "sha256": "sha256:312f02d4ad6f0189d3195ad788ded7ed08684b835c17ad0095940807d3c6bb80", "bytes": 56142, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-06756-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12267434", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE177034", "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=GSE177034", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE177034", "version": null, "note": "The dataset(GSE177034) employed in this study are available via the GEO database (GeneExpressionOmnibus, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE177034). Genes related to pyroptosis were sourced from earlier investigations(10.1038/nri3452, 10.1038/s41420-021-00451-x, 10.1016/j.jsb.2017.08.001, 10.1038/s41568-019-0123-y, 10.1038/s41419-019-1883-8, 10.1111/imr.12296).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset(GSE177034) employed in this study are available via the GEO database (GeneExpressionOmnibus, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE177034). Genes related to pyroptosis were sourced from earlier investigations(10.1038/nri3452, 10.1038/s41420-021-00451-x, 10.1016/j.jsb.2017.08.001, 10.1038/s41568-019-0123-y, 10.1038/s41419-019-1883-8, 10.1111/imr.12296).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5370696", "GSM5370697", "GSM5370698", "GSM5370699", "GSM5370700", "GSM5370701", "GSM5370702", "GSM5370703", "GSM5370704", "GSM5370705", "GSM5370706", "GSM5370707", "GSM5370708", "GSM5370709", "GSM5370710", "GSM5370711", "GSM5370712", "GSM5370713", "GSM5370714", "GSM5370715", "GSM5370716", "GSM5370717", "GSM5370718", "GSM5370719", "GSM5370720", "GSM5370721", "GSM5370722", "GSM5370723", "GSM5370724", "GSM5370725", "GSM5370726", "GSM5370727", "GSM5370728", "GSM5370729", "GSM5370730", "GSM5370731", "GSM5370732", "GSM5370733", "GSM5370734", "GSM5370735", "GSM5370736", "GSM5370737", "GSM5370738", "GSM5370739", "GSM5370740", "GSM5370741", "GSM5370742", "GSM5370743", "GSM5370744", "GSM5370745", "GSM5370746", "GSM5370747", "GSM5370748", "GSM5370749", "GSM5370750", "GSM5370751", "GSM5370752", "GSM5370753", "GSM5370754", "GSM5370755", "GSM5370756", "GSM5370757", "GSM5370758", "GSM5370759", "GSM5370760", "GSM5370761", "GSM5370762", "GSM5370763", "GSM5370764", "GSM5370765", "GSM5370766", "GSM5370767", "GSM5370768", "GSM5370769", "GSM5370770", "GSM5370771", "GSM5370772", "GSM5370773", "GSM5370774", "GSM5370775", "GSM5370776", "GSM5370777", "GSM5370778", "GSM5370779", "GSM5370780", "GSM5370781", "GSM5370782", "GSM5370783", "GSM5370784", "GSM5370785", "GSM5370786", "GSM5370787", "GSM5370788", "GSM5370789", "GSM5370790", "GSM5370791", "GSM5370792", "GSM5370793", "GSM5370794", "GSM5370795", "GSM5370796", "GSM5370797", "GSM5370798", "GSM5370799", "GSM5370800", "GSM5370801", "GSM5370802", "GSM5370803", "GSM5370804", "GSM5370805", "GSM5370806", "GSM5370807", "GSM5370808", "GSM5370809", "GSM5370810", "GSM5370811", "GSM5370812", "GSM5370813", "GSM5370814", "GSM5370815", "GSM5370816", "GSM5370817", "GSM5370818", "GSM5370819", "GSM5370820", "GSM5370821", "GSM5370822", "GSM5370823", "GSM5370824", "GSM5370825", "GSM5370826", "GSM5370827", "GSM5370828", "GSM5370829", "GSM5370830", "GSM5370831", "GSM5370832", "GSM5370833", "GSM5370834", "GSM5370835", "GSM5370836", "GSM5370837", "GSM5370838", "GSM5370839", "GSM5370840", "GSM5370841", "GSM5370842", "GSM5370843", "GSM5370844", "GSM5370845", "GSM5370846", "GSM5370847", "GSM5370848", "GSM5370849", "GSM5370850", "GSM5370851", "GSM5370852", "GSM5370853", "GSM5370854", "GSM5370855", "GSM5370856", "GSM5370857", "GSM5370858", "GSM5370859", "GSM5370860", "GSM5370861", "GSM5370862", "GSM5370863", "GSM5370864", "GSM5370865", "GSM5370866", "GSM5370867", "GSM5370868", "GSM5370869", "GSM5370870", "GSM5370871", "GSM5370872", "GSM5370873", "GSM5370874", "GSM5370875", "GSM5370876", "GSM5370877", "GSM5370878", "GSM5370879", "GSM5370880", "GSM5370881", "GSM5370882", "GSM5370883", "GSM5370884", "GSM5370885", "GSM5370886", "GSM5370887", "GSM5370888", "GSM5370889", "GSM5370890", "GSM5370891"], "sample_count": 196, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Acute Inflammatory Response via Neutrophil Activation Protects Against the Development of Chronic Pain", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE177034 not downloaded", "asset:data:geo:GSE177034 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "reordered", "quote": "Statistical analysis was performed using R software, version 4.1.2. The Spearman correlation test was selected to ascertain the correlation between two variables. Comparisons between the two groups were made with the Wilcoxon test. Comparisons between three or more groups were made with the Kruskal–Wallis test. A two-tailed p-value of < 0.05 was indicative of statistical significance. The ‘pROC’ R package was used to create ROC curves and determine AUC values for the feature genes, thus assessing their potential as diagnostic indicators24."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE177034"], "resolved_accessions": ["GSE177034"], "statements": ["The dataset(GSE177034) employed in this study are available via the GEO database (GeneExpressionOmnibus, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE177034). Genes related to pyroptosis were sourced from earlier investigations(10.1038/nri3452, 10.1038/s41420-021-00451-x, 10.1016/j.jsb.2017.08.001, 10.1038/s41568-019-0123-y, 10.1038/s41419-019-1883-8, 10.1111/imr.12296)."], "basis": "The paper names GSE177034 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40670404", "data:geo:GSE177034"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE177034"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:57:04Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15043, "completion_tokens": 1578, "cached_tokens": 256}}, "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:40670404", "type": "paper", "label": "pmid:40670404"}, {"id": "source:pmid:40670404", "type": "manuscript", "label": "PMID 40670404 full text"}, {"id": "data:geo:GSE177034", "type": "dataset", "label": "GEO GSE177034"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40670404", "type": "paper", "label": "pmid:40670404"}, {"id": "source:pmid:40670404", "type": "manuscript", "label": "PMID 40670404 full text"}, {"id": "data:geo:GSE177034", "type": "dataset", "label": "GEO GSE177034"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40670404", "type": "extraction", "used": ["source:pmid:40670404"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE177034", "type": "accession_resolution", "used": ["data:geo:GSE177034"], "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:40670404", "parent_hash": "sha256:3674d62b58fb9305bbca12573a358b6d168339bbcf75bdf5706ca9c16fd5057c", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE177034 licence not read", "asset:data:geo:GSE177034 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Statistical analysis was performed using R software, version 4.1.2. The Spearman correlation test was selected to ascertain the correlation between two variables. Comparisons between the two groups were made with the Wilcoxon test. Comparisons between three or more groups were made with the Kruskal–Wallis test. A two-tailed p-value of < 0.05 was indicative of statistical significance. The ‘pROC’ R package was used to create ROC curves and determine AUC values for the feature genes, thus assessing their potential as diagnostic indicators24."], "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":"2026-11-04T03:15:18+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}}}