{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37291580", "kind": "science-record", "revision": 4, "content_hash": "sha256:a6ec13d0a5e4e7b85ac1b5d1d642389e22522c760791f2002ad8dadf9c885c3d", "created_at": "2026-11-01T19:02:01Z", "updated_at": "2026-11-01T22:52:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the molecular mechanism of comorbidity of autism spectrum disorder and inflammatory bowel disease by combining multiple data sets.", "doi": "10.1186/s12967-023-04218-z", "pmid": "37291580", "authors": ["Jinyi Zhu", "Haoran Meng", "Li Zhang", "Yan Li"], "journal": "Journal of translational medicine", "year": 2023, "abstract": "BACKGROUND: Autism spectrum disorder (ASD) is a neurodevelopmental disorder that is difficult to diagnose. Inflammatory bowel disease (IBD) is a common chronic digestive disease. Previous studies have shown a potential correlation between ASD and IBD, but the pathophysiological mechanism remains unclear. The purpose of this research was to examine the biological mechanisms underlying the differentially expressed genes (DEGs) of ASD and IBD using bioinformatics tools.\nMETHODS: Limma software was used to evaluate the DEGs between ASD and IBD. The GSE3365, GSE18123, and GSE150115 microarray data sets were acquired from the Gene Expression Omnibus (GEO) database. We then performed 6 analyses, namely, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation; weighted gene coexpression network analysis; correlation analysis of hub genes with autophagy, ferroptosis and immunity; transcriptional regulation analysis of hub genes; single-cell sequencing analysis; and potential therapeutic drug prediction.\nRESULTS: A total of 505 DEGs associated with ASD and 616 DEGs associated with IBD were identified, and 7 genes overlapped between these sets. GO and KEGG analyses revealed several pathways enriched in both diseases. A total of 98 common genes related to ASD and IBD were identified by weighted gene coexpression network analysis (WGCNA), and 4 hub genes were obtained by intersection with the 7 intersecting DEGs, which were PDGFC, CA2, GUCY1B3 and SDPR. We also found that 4 hub genes in the two diseases were related to autophagy, ferroptosis or immune factors. In addition, motif-TF annotation analysis showed that cisbp__M0080 was the most relevant motif. We also used the Connectivity Map (CMap) database to identify 4 potential therapeutic agents.\nCONCLUSION: This research reveals the shared pathogenesis of ASD and IBD. In the future, these common hub genes may provide new targets for further mechanistic research as well as new therapies for patients with ASD and IBD.", "claims": [{"id": "claim-method", "statement": "The limma package [10] was used to compare the normal and disease-affected groups, and the screening criteria for DEGs were P value < 0.05 and |logFC|>0.585.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37291580", "locator": "sections[3] \"Data download\" paragraph 2", "quote": "The limma package [10] was used to compare the normal and disease-affected groups, and the screening criteria for DEGs were P value < 0.05 and |logFC|>0.585."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The Series Matrix File data file of GSE18123 was downloaded from the NCBI GEO public database [9].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37291580", "locator": "sections[3] \"Data download\" paragraph 2", "quote": "The Series Matrix File data file of GSE18123 was downloaded from the NCBI GEO public database [9]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 98 common genes related to ASD and IBD were identified by weighted gene coexpression network analysis (WGCNA), and 4 hub genes were obtained by intersection with the 7 intersecting DEGs, which were PDGFC, CA2, GUCY1B3 and SDPR.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37291580", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 98 common genes related to ASD and IBD were identified by weighted gene coexpression network analysis (WGCNA), and 4 hub genes were obtained by intersection with the 7 intersecting DEGs, which were PDGFC, CA2, GUCY1B3 and SDPR."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 98 common genes related to ASD and IBD were identified by weighted gene coexpression network analysis (WGCNA), and 4 hub genes were obtained by intersection with the 7 intersecting DEGs, which were PDGFC, CA2, GUCY1B3 and SDPR.", "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:37291580"], "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:GSE150115"], "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:GSE150115"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37291580", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12967-023-04218-z", "sha256": "sha256:46c4cb1357e11da9120e2ecd0e3eb98cbde217c1af114847aae9efc9c0977088", "bytes": 32932, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12967-023-04218-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10249282", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE150115", "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=GSE150115", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE150115", "version": null, "note": "The Series Matrix File data file of GSE18123 was downloaded from the NCBI GEO public database [9].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Series Matrix File data file of GSE18123 was downloaded from the NCBI GEO public database [9].", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM4523789", "GSM4523790", "GSM4523791", "GSM4523792", "GSM4523793"], "sample_count": 5, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE18123", "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=GSE18123", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE18123", "version": null, "note": "The Series Matrix File data file of GSE18123 was downloaded from the NCBI GEO public database [9].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Series Matrix File data file of GSE18123 was downloaded from the NCBI GEO public database [9].", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM650510", "GSM650512", "GSM650513", "GSM650514", "GSM650515", "GSM650516", "GSM650517", "GSM650518", "GSM650519", "GSM650520", "GSM650521", "GSM650522", "GSM650523", "GSM650525", "GSM650526", "GSM650527", "GSM650528", "GSM650529", "GSM650530", "GSM650531", "GSM650532", "GSM650533", "GSM650534", "GSM650536", "GSM650537", "GSM650538", "GSM650540", "GSM650541", "GSM650542", "GSM650543", "GSM650544", "GSM650545", "GSM650546", "GSM650547", "GSM650548", "GSM650549", "GSM650550", "GSM650551", "GSM650552", "GSM650553", "GSM650554", "GSM650555", "GSM650556", "GSM650557", "GSM650558", "GSM650560", "GSM650561", "GSM650562", "GSM650563", "GSM650564", "GSM650565", "GSM650566", "GSM650567", "GSM650568", "GSM650569", "GSM650570", "GSM650571", "GSM650572", "GSM650573", "GSM650574", "GSM650575", "GSM650577", "GSM650578", "GSM650579", "GSM650580", "GSM650581", "GSM650600", "GSM650603", "GSM650604", "GSM650606", "GSM650607", "GSM650614", "GSM650615", "GSM650617", "GSM650618", "GSM650619", "GSM650620", "GSM650621", "GSM650622", "GSM650632", "GSM650633", "GSM650636", "GSM650637", "GSM650638", "GSM650639", "GSM650640", "GSM650641", "GSM650642", "GSM650643", "GSM650644", "GSM650645", "GSM650646", "GSM650647", "GSM650648", "GSM650649", "GSM650651", "GSM650652", "GSM650653", "GSM650654", "GSM650655", "GSM650656", "GSM650657", "GSM650658", "GSM650659", "GSM650660", "GSM650661", "GSM650662", "GSM650663", "GSM650664", "GSM650665", "GSM650666", "GSM650667", "GSM650668", "GSM650669", "GSM650670", "GSM650671", "GSM650672", "GSM650673", "GSM650674", "GSM650675", "GSM650676", "GSM650677", "GSM650678", "GSM650679", "GSM650680", "GSM650681", "GSM650682", "GSM650683", "GSM650684", "GSM650685", "GSM650686", "GSM650687", "GSM650688", "GSM650689", "GSM650690", "GSM650691", "GSM650692", "GSM650693", "GSM650694", "GSM650695", "GSM650696", "GSM650697", "GSM650698", "GSM650699", "GSM650700", "GSM650701", "GSM650702", "GSM650703", "GSM650704", "GSM650705", "GSM650706", "GSM650707", "GSM650708", "GSM650709", "GSM650712", "GSM650713", "GSM650714", "GSM650715", "GSM650716", "GSM650717", "GSM650718", "GSM650719", "GSM650720", "GSM650721", "GSM650722", "GSM650723", "GSM650724", "GSM650725", "GSM650726", "GSM650727", "GSM650728", "GSM650729", "GSM650730", "GSM650731", "GSM650732", "GSM650733", "GSM650734", "GSM650735", "GSM650737", "GSM650740", "GSM650744", "GSM650748", "GSM650750", "GSM650752", "GSM650753", "GSM650758", "GSM650760", "GSM650761", "GSM650762", "GSM650763", "GSM650764", "GSM650765", "GSM650766", "GSM650767", "GSM650768", "GSM650769", "GSM650770", "GSM650771", "GSM650772", "GSM650773", "GSM650801", "GSM650802", "GSM650806", "GSM650808", "GSM650809", "GSM650813", "GSM650816", "GSM650818", "GSM650819", "GSM650820", "GSM650821", "GSM650822", "GSM650823", "GSM650824", "GSM650825", "GSM650826", "GSM650827", "GSM650828", "GSM650829", "GSM650830", "GSM650831", "GSM650832", "GSM650833", "GSM650834", "GSM650835", "GSM650836", "GSM650837", "GSM650838", "GSM650839", "GSM650840", "GSM650841", "GSM650842", "GSM650843", "GSM650844", "GSM650845", "GSM650846", "GSM650847", "GSM650848", "GSM650849", "GSM650850", "GSM650851", "GSM650852", "GSM650853", "GSM650854", "GSM650855", "GSM650856", "GSM650857", "GSM650858", "GSM650859", "GSM650860", "GSM650861", "GSM650863", "GSM650864", "GSM650865", "GSM650866", "GSM650867", "GSM650868", "GSM650869", "GSM650870", "GSM650871", "GSM650872", "GSM650873", "GSM650874", "GSM650875", "GSM650876", "GSM650877", "GSM650878", "GSM650879", "GSM650880", "GSM650883", "GSM650885", "GSM650923", "GSM650924", "GSM650930", "GSM650931", "GSM650944", "GSM650946", "GSM650950", "GSM650951", "GSM650954", "GSM650959", "GSM650968", "GSM650969", "GSM650970", "GSM650975"], "sample_count": 285, "group_sizes": null, "group_sizes_basis": null, "platform": "6244;570", "taxon": "Homo sapiens", "title": "Blood gene expression signatures distinguish autism spectrum disorders from controls", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE3365", "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=GSE3365", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE3365", "version": null, "note": "The Series Matrix File data file of GSE18123 was downloaded from the NCBI GEO public database [9].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Series Matrix File data file of GSE18123 was downloaded from the NCBI GEO public database [9].", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM76030", "GSM76031", "GSM76032", "GSM76033", "GSM76034", "GSM76035", "GSM76036", "GSM76037", "GSM76038", "GSM76039", "GSM76040", "GSM76041", "GSM76042", "GSM76043", "GSM76044", "GSM76045", "GSM76046", "GSM76047", "GSM76048", "GSM76049", "GSM76050", "GSM76051", "GSM76052", "GSM76053", "GSM76054", "GSM76055", "GSM76056", "GSM76057", "GSM76058", "GSM76059", "GSM76060", "GSM76061", "GSM76062", "GSM76063", "GSM76064", "GSM76065", "GSM76066", "GSM76067", "GSM76068", "GSM76069", "GSM76070", "GSM76071", "GSM76072", "GSM76073", "GSM76074", "GSM76075", "GSM76076", "GSM76077", "GSM76078", "GSM76079", "GSM76080", "GSM76081", "GSM76082", "GSM76083", "GSM76084", "GSM76085", "GSM76086", "GSM76087", "GSM76088", "GSM76089", "GSM76090", "GSM76091", "GSM76092", "GSM76093", "GSM76094", "GSM76095", "GSM76096", "GSM76097", "GSM76098", "GSM76099", "GSM76100", "GSM76101", "GSM76102", "GSM76103", "GSM76104", "GSM76105", "GSM76106", "GSM76107", "GSM76108", "GSM76109", "GSM76110", "GSM76111", "GSM76112", "GSM76113", "GSM76114", "GSM76115", "GSM76116", "GSM76117", "GSM76118", "GSM76119", "GSM76120", "GSM76121", "GSM76122", "GSM76123", "GSM76124", "GSM76125", "GSM76126", "GSM76127", "GSM76128", "GSM76129", "GSM76130", "GSM76131", "GSM76132", "GSM76133", "GSM76134", "GSM76135", "GSM76136", "GSM76137", "GSM76138", "GSM76139", "GSM76140", "GSM76141", "GSM76142", "GSM76143", "GSM76144", "GSM76145", "GSM76146", "GSM76147", "GSM76148", "GSM76149", "GSM76150", "GSM76151", "GSM76152", "GSM76153", "GSM76154", "GSM76155", "GSM76156"], "sample_count": 127, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Comparison of PBMCs in Inflammatory Bowel Disease", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE150115 not downloaded", "asset:data:geo:GSE150115 licence not read", "asset:data:geo:GSE18123 not downloaded", "asset:data:geo:GSE18123 licence not read", "asset:data:geo:GSE3365 not downloaded", "asset:data:geo:GSE3365 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 limma package [10] was used to compare the normal and disease-affected groups, and the screening criteria for DEGs were P value < 0.05 and |logFC|>0.585."}}], "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": ["GSE18123", "GSE3365", "GSE150115"], "resolved_accessions": ["GSE18123", "GSE3365", "GSE150115"], "statements": ["The Series Matrix File data file of GSE18123 was downloaded from the NCBI GEO public database [9]."], "basis": "The paper names GSE18123, GSE3365, GSE150115 in NCBI GEO public database 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:37291580", "data:geo:GSE150115"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE150115"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:43:24Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 8945, "completion_tokens": 2165, "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:37291580", "type": "paper", "label": "pmid:37291580"}, {"id": "source:pmid:37291580", "type": "manuscript", "label": "PMID 37291580 full text"}, {"id": "data:geo:GSE150115", "type": "dataset", "label": "GEO GSE150115"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37291580", "type": "paper", "label": "pmid:37291580"}, {"id": "source:pmid:37291580", "type": "manuscript", "label": "PMID 37291580 full text"}, {"id": "data:geo:GSE150115", "type": "dataset", "label": "GEO GSE150115"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37291580", "type": "extraction", "used": ["source:pmid:37291580"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE150115", "type": "accession_resolution", "used": ["data:geo:GSE150115"], "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:37291580", "parent_hash": "sha256:37732505da521860287f949305417eba507bae1c9440b4aa952e4a236ebb5abc", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE150115 licence not read", "asset:data:geo:GSE150115 not downloaded", "asset:data:geo:GSE18123 licence not read", "asset:data:geo:GSE18123 not downloaded", "asset:data:geo:GSE3365 licence not read", "asset:data:geo:GSE3365 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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 limma package [10] was used to compare the normal and disease-affected groups, and the screening criteria for DEGs were P value < 0.05 and |logFC|>0.585."], "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":"2026-11-04T02:43:51+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}}}