{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32355739", "kind": "science-record", "revision": 9, "content_hash": "sha256:d993c5e93276df9893130bf2b367466730ad51e55fc173104910e469805eb846", "created_at": "2026-11-01T15:41:00Z", "updated_at": "2026-11-01T22:44:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of potential hub genes involved in the pathogenesis of Chinese type 1 diabetic patients.", "doi": "10.21037/atm.2020.02.171", "pmid": "32355739", "authors": ["Shuting Yang", "Chuqing Cao", "Zhiguo Xie", "Zhiguang Zhou"], "journal": "Annals of translational medicine", "year": 2020, "abstract": "BACKGROUND: Type 1 diabetes is an autoimmune disease strongly related to genetic factors. Although studies on T1D susceptibility genes have achieved great progress, the molecular mechanism of T1D remains to be explained.\nMETHODS: To explore the underlying mechanisms of T1D, bioinformatic analysis based on a microarray database was used to determine the key biomarkers of T1D as well as their biofunctions and interactions. The microarray database GSE55100 was downloaded from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were processed by packages in R Software. The database for Annotation, Visualization, and Integrated Discovery (DAVID, version 6.8) was used to conduct gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The protein-protein interaction network was analyzed with the Search Tool for the Retrieval of Interacting Genes (STRING), and the module analysis was performed using Cytoscape.\nRESULTS: Seventy-eight DEGs and 13 hub genes were identified. The biofunctions and pathways of these DEGs were enriched in immune response, extracellular exosome, cytokine activity and antigen processing and presentation. Thirteen DEGs with MCODE score ≥2 were selected as hub genes including MMP9, ARG1, CAMP, CHI3L1, CRISP3, SLPI, LCN2, PGLYRP1, LTF, RETN, CEACAM1, CEACAM8 and MS4A3.\nCONCLUSIONS: The identification and analyses of the DEGs and hub genes from database GSE55100 provide novel prospectives of the pathogenesis of T1D.", "claims": [{"id": "claim-method", "statement": "The affy package in R Software was used for data normalization, and limma package was applied for the remaining processes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32355739", "locator": "sections[4] \"DEG identification\" paragraph 2", "quote": "The affy package in R Software was used for data normalization, and limma package was applied for the remaining processes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mRNA expression file of GSE55100 was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), a public data source recoding genetic information (11). Transcriptome data were obtained from the GPL570 platform, Affymetrix Human Genome U133 Plus 2.0 Array. The annotation file in the platform matches the probes with the corresponding genes. GSE55100 contains the mRNA information of PBMCs from 12 patients with newly diagnosed T1D and 10 normal controls. The affy package in R Software was used for data normalization, and limma package was applied for the remaining processes. Genes with the P<0.05 and |log Fc| (fold change) >1 were considered as DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32355739", "locator": "sections[3] \"Data resources\" paragraph 2", "quote": "The mRNA expression file of GSE55100 was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), a public data source recoding genetic information (11)."}, {"asset": "source:pmid:32355739", "locator": "sections[3] \"Data resources\" paragraph 2", "quote": "Transcriptome data were obtained from the GPL570 platform, Affymetrix Human Genome U133 Plus 2.0 Array."}, {"asset": "source:pmid:32355739", "locator": "sections[3] \"Data resources\" paragraph 2", "quote": "The annotation file in the platform matches the probes with the corresponding genes."}, {"asset": "source:pmid:32355739", "locator": "sections[3] \"Data resources\" paragraph 2", "quote": "GSE55100 contains the mRNA information of PBMCs from 12 patients with newly diagnosed T1D and 10 normal controls."}, {"asset": "source:pmid:32355739", "locator": "sections[4] \"DEG identification\" paragraph 2", "quote": "The affy package in R Software was used for data normalization, and limma package was applied for the remaining processes."}, {"asset": "source:pmid:32355739", "locator": "sections[4] \"DEG identification\" paragraph 2", "quote": "Genes with the P<0.05 and |log Fc| (fold change) >1 were considered as DEGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32355739"], "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:GSE55100"], "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:GSE55100"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32355739", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm.2020.02.171", "sha256": "sha256:535ef91d61935abb5e8b4213d17fd1a0b4f4587eb7ab93e48a2d4ed945e29488", "bytes": 30078, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/atm.2020.02.171", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7186604", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE55100", "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=GSE55100", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE55100", "version": null, "note": "The mRNA expression file of GSE55100 was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), a public data source recoding genetic information (11). Transcriptome data were obtained from the GPL570 platform, Affymetrix Human Genome U133 Plus 2.0 Array. The annotation file in the platform matches the probes with the corresponding genes. GSE55100 contains the mRNA information of PBMCs from 12 patients with newly diagnosed T1D and 10 normal controls. The affy package in R Software was used for data normalization, and limma package was applied for the remaining processes. Genes with the P<0.05 and |log Fc| (fold change) >1 were considered as DEGs.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mRNA expression file of GSE55100 was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), a public data source recoding genetic information (11). Transcriptome data were obtained from the GPL570 platform, Affymetrix Human Genome U133 Plus 2.0 Array. The annotation file in the platform matches the probes with the corresponding genes. GSE55100 contains the mRNA information of PBMCs from 12 patients with newly diagnosed T1D and 10 normal controls. The affy package in R Software was used for data normalization, and limma package was applied for the remaining processes. 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"version": null, "note": "Results of GO and KEGG pathway enrichment analysis of DEGs", "structure": {"pmcid": "PMC7186604", "section_index": 9, "section_title": "Enrichment analyses", "row_count": 18, "column_count": 4}, "table": {"label": "Table 1", "caption": "Results of GO and KEGG pathway enrichment analysis of DEGs", "rows": [["Term", "Description", "Count in gene set", "P value"], ["GO:0006955", "Immune response", "11", "4.61E-06"], ["GO:0045087", "Innate immune response", "10", "3.91E-05"], ["GO:0007155", "Cell adhesion", "9", "3.78E-04"], ["GO:0006954", "Inflammatory response", "8", "6.38E-04"], ["GO:0008284", "Positive regulation of cell proliferation", "7", "0.009180343"], ["GO:0070062", "Extracellular exosome", "28", "7.73E-07"], ["GO:0005615", "Extracellular space", "22", "7.20E-09"], ["GO:0005576", "Extracellular region", "14", "0.005261967"], ["GO:0005887", "Integral component of plasma membrane", "12", "0.013566932"], ["GO:0005125", "Cytokine activity", "5", "0.004714656"], ["GO:0005506", "Iron ion binding", "4", "0.021178215"], ["GO:0030246", "Carbohydrate binding", "4", "0.039835718"], ["GO:0004888", "Transmembrane signaling receptor activity", "4", "0.049477271"], ["GO:0004252", "Serine-type endopeptidase activity", "4", "0.075232402"], ["hsa04612", "Antigen processing and presentation", "5", "3.45E-04"], ["hsa05164", "Influenza A", "5", "0.007298983"], ["hsa05168", "Herpes simplex infection", "5", "0.008696934"]], "row_count": 18, "column_count": 4, "numeric_cells": 51, "header_rows": 1, "locator": "section[9]/table-wrap[1]#t1"}}, {"id": "asset:table:pmid:32355739:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8d5c6044f3378ab971bfb866c462dc9fb2bf891d615b4f5438e650bf8c53541d", "bytes": 1798, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#t2", "version": null, "note": "Information of 13 hub genes in T1D", "structure": {"pmcid": "PMC7186604", "section_index": 11, "section_title": "Hub gene selection", "row_count": 14, "column_count": 3}, "table": {"label": "Table 2", "caption": "Information of 13 hub genes in T1D", "rows": [["Gene symbol", "Full name", "Implications"], ["MMP9", "Matrix metallopeptidase 9", "The activation of MMP9 is related with the severity of stroke in T1D"], ["ARG1", "Arginase 1", "ARG1 expression increases in T1D patients with complications"], ["CAMP", "Cathelicidin antimicrobial peptide", "CAMP was upregulated in the jejunum in low-antigen hydrolyzed casein diet T1D rats"], ["CHI3L1", "Chitinase 3 like 1", "The serum level of CHI3L1 was elevated in subjects with diabetic retinopathy"], ["CRISP3", "Cysteine-rich secretory protein 3", "The association between CRISP3 and T1D has not been reported"], ["SLPI", "Secretory leukocyte peptidase inhibitor", "The association between SLPI and T1D has not been reported"], ["LCN2", "Lipocalin 2", "The serum concentration of LCN2 correlated positively with systolic arterial pressure but negatively with eGRF in T1D patients"], ["PGLYRP1", "Peptidoglycan recognition protein 1", "The association between PGLYRP1 and T1D has not been reported"], ["LTF", "Lactotransferrin", "The association between LTF and T1D has not been reported"], ["RETN", "Resistin", "The resistin levels were elevated in T1DM patients and normalized by islet transplantation"], ["CEACAM1", "Carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)", "The association between CEACAM1 and T1D has not been reported"], ["CEACAM8", "Carcinoembryonic antigen-related cell adhesion molecule 8", "The association between CEACAM8 and T1D has not been reported"], ["MS4A3", "Membrane-spanning 4-domains, subfamily A, member 3 (hematopoietic cell-specific)", "The association between MS4A3 and T1D has not been reported"]], "row_count": 14, "column_count": 3, "numeric_cells": 9, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t2"}}], "gaps": ["asset:data:geo:GSE55100 not downloaded", "asset:data:geo:GSE55100 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The affy package in R Software was used for data normalization, and limma package was applied for the remaining processes."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE55100"], "resolved_accessions": ["GSE55100"], "statements": ["The mRNA expression file of GSE55100 was downloaded from GEO database (http://www.ncbi.nlm.nih.gov/geo), a public data source recoding genetic information (11). Transcriptome data were obtained from the GPL570 platform, Affymetrix Human Genome U133 Plus 2.0 Array. The annotation file in the platform matches the probes with the corresponding genes. GSE55100 contains the mRNA information of PBMCs from 12 patients with newly diagnosed T1D and 10 normal controls. The affy package in R Software was used for data normalization, and limma package was applied for the remaining processes. Genes with the P<0.05 and |log Fc| (fold change) >1 were considered as DEGs."], "basis": "The paper names GSE55100 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32355739", "data:geo:GSE55100", "asset:table:pmid:32355739:1", "asset:table:pmid:32355739:2", "asset:table:pmid:32355739:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE55100"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:19:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 24168, "completion_tokens": 1382, "cached_tokens": 776}}, "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:32355739", "type": "paper", "label": "pmid:32355739"}, {"id": "source:pmid:32355739", "type": "manuscript", "label": "PMID 32355739 full text"}, {"id": "data:geo:GSE55100", "type": "dataset", "label": "GEO GSE55100"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32355739", "type": "paper", "label": "pmid:32355739"}, {"id": "source:pmid:32355739", "type": "manuscript", "label": "PMID 32355739 full text"}, {"id": "data:geo:GSE55100", "type": "dataset", "label": "GEO GSE55100"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32355739", "type": "extraction", "used": ["source:pmid:32355739"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE55100", "type": "accession_resolution", "used": ["data:geo:GSE55100"], "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:32355739", "parent_hash": "sha256:2618a63c6ef2b9599f7c374bcc618b3a1a5f39572a8bc19242906e482b342a2c", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE55100 licence not read", "asset:data:geo:GSE55100 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ms of T1D, bioinformatic analysis based on a microarray database was used to determine the key bioma", "as their biofunctions and interactions. The microarray database GSE55100 was downloaded from the Ge"], "order_basis": "paper_text_order:362", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The affy package in R Software was used for data normalization, and limma package was applied for the remaining processes."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T04:15:48+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}}}