{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38809509", "kind": "science-record", "revision": 2, "content_hash": "sha256:cba1dea9ca08bb6a95506277c7a0c131a438e0d5b58009a91b4eda2495c702bf", "created_at": "2026-11-01T19:20:46Z", "updated_at": "2026-11-01T21:33:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Leveraging pQTL-based Mendelian randomization to identify new treatment prospects for primary biliary cholangitis and primary sclerosing cholangitis.", "doi": "10.18632/aging.205867", "pmid": "38809509", "authors": ["Lei Dai", "Yunyan Ye", "Joseph Mugaany", "Zetong Hu", "Jing Huang", "Changjiang Lu"], "journal": "Aging", "year": 2024, "abstract": "Primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) are autoimmune disorders characterized by progressive and chronic damage to the bile ducts, presenting clinicians with significant challenges. The objective of this study is to identify potential druggable targets to offer new avenues for treatment. A Mendelian randomization analysis was performed to identify druggable targets for PBC and PSC. This involved obtaining Cis-protein quantitative trait loci (Cis-pQTL) data from the deCODE database to serve as exposure. Outcome data for PBC (557 cases and 281,127 controls) and PSC (1,715 cases and 330,903 controls) were obtained from the FINNGEN database. Colocalization analysis was conducted to determine whether these features share the same associated SNPs. Validation of the expression level of druggable targets was done using the GSE119600 dataset and immunohistochemistry for clinical samples. Lastly, the DRUGBANK database was used to predict potential drugs. The MR analysis identified eight druggable targets each for PBC and PSC. Subsequent summary-data-based MR and colocalization analyses showed that LEFTY2 had strong evidence as a therapeutic candidate for PBC, while HSPB1 had moderate evidence. For PSC, only FCGR3B showed strong evidence as a therapeutic candidate. Additionally, upregulated expression of these genes was validated in PBC and PSC groups by GEO dataset and clinical samples. This study identifies two novel druggable targets with strong evidence for therapeutic candidates for PBC (LEFTY2 and HSPB1) and one for PSC (FCGR3B). These targets offer new therapeutic opportunities to address the challenging nature of PBC and PSC treatment.", "claims": [{"id": "claim-method", "statement": "Two-sample Mendelian randomization analysis was conducted using the TwoSampleMR package [29].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38809509", "locator": "sections[7] \"Two-sample Mendelian randomization\" paragraph 2", "quote": "Two-sample Mendelian randomization analysis was conducted using the TwoSampleMR package [29]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s. All data and original files in our work are freely available under a ‘Creative Commons BY 4.0’ license. All methods were carried out in accordance with relevant guidelines and regulations.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38809509", "locator": "sections[14] \"Availability of data and materials\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s. All data and original files in our work are freely available under a ‘Creative Commons BY 4.0’ license. All methods were carried out in accordance with relevant guidelines and regulations."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This study identifies two novel druggable targets with strong evidence for therapeutic candidates for PBC (LEFTY2 and HSPB1) and one for PSC (FCGR3B).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38809509", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This study identifies two novel druggable targets with strong evidence for therapeutic candidates for PBC (LEFTY2 and HSPB1) and one for PSC (FCGR3B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This study identifies two novel druggable targets with strong evidence for therapeutic candidates for PBC (LEFTY2 and HSPB1) and one for PSC (FCGR3B).", "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:38809509"], "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:GSE119600"], "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:GSE119600"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38809509", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.205867", "sha256": "sha256:19d692ec2b516bd5a7fcb513be81e4ddb101a4f191bbcf45df325e4b42d95b1f", "bytes": 41428, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.205867", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11164478", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE119600", "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=GSE119600", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE119600", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s. All data and original files in our work are freely available under a ‘Creative Commons BY 4.0’ license. All methods were carried out in accordance with relevant guidelines and regulations.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s. All data and original files in our work are freely available under a ‘Creative Commons BY 4.0’ license. All methods were carried out in accordance with relevant guidelines and regulations.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3378086", "GSM3378093", "GSM3378095", "GSM3378097", "GSM3378099", "GSM3378101", "GSM3378103", "GSM3378105", "GSM3378107", "GSM3378109", "GSM3378111", "GSM3378112", "GSM3378115", "GSM3378118", "GSM3378120", "GSM3378121", "GSM3378124", "GSM3378126", "GSM3378128", "GSM3378130", "GSM3378132", "GSM3378134", "GSM3378136", "GSM3378138", "GSM3378140", "GSM3378141", "GSM3378143", "GSM3378146", "GSM3378148", "GSM3378150", "GSM3378152", "GSM3378154", "GSM3378156", "GSM3378158", "GSM3378160", "GSM3378162", "GSM3378164", "GSM3378166", "GSM3378167", "GSM3378169", "GSM3378171", "GSM3378173", "GSM3378175", "GSM3378177", "GSM3378179", "GSM3378181", "GSM3378183", "GSM3378185", "GSM3378187", "GSM3378188", "GSM3378189", "GSM3378190", "GSM3378191", "GSM3378192", "GSM3378193", "GSM3378194", "GSM3378195", "GSM3378196", "GSM3378197", "GSM3378198", "GSM3378199", "GSM3378200", "GSM3378201", "GSM3378202", "GSM3378203", "GSM3378204", "GSM3378205", "GSM3378206", "GSM3378207", "GSM3378208", "GSM3378209", "GSM3378210", "GSM3378211", "GSM3378212", "GSM3378213", "GSM3378214", "GSM3378215", "GSM3378216", "GSM3378217", "GSM3378218", "GSM3378219", "GSM3378220", "GSM3378221", "GSM3378222", "GSM3378223", "GSM3378224", "GSM3378225", "GSM3378226", "GSM3378227", "GSM3378228", "GSM3378229", "GSM3378230", "GSM3378231", "GSM3378232", "GSM3378233", "GSM3378234", "GSM3378235", "GSM3378236", "GSM3378237", "GSM3378238", "GSM3378239", "GSM3378240", "GSM3378241", "GSM3378242", "GSM3378243", "GSM3378244", "GSM3378245", "GSM3378246", "GSM3378247", "GSM3378248", "GSM3378249", "GSM3378250", "GSM3378251", "GSM3378252", "GSM3378253", "GSM3378254", "GSM3378255", "GSM3378256", "GSM3378257", "GSM3378258", "GSM3378259", "GSM3378260", "GSM3378261", "GSM3378262", "GSM3378263", "GSM3378264", "GSM3378265", "GSM3378266", "GSM3378267", "GSM3378268", "GSM3378269", "GSM3378270", "GSM3378271", "GSM3378272", "GSM3378273", "GSM3378274", "GSM3378275", "GSM3378276", "GSM3378277", "GSM3378278", "GSM3378279", "GSM3378280", "GSM3378281", "GSM3378282", "GSM3378283", "GSM3378284", "GSM3378285", "GSM3378286", "GSM3378287", "GSM3378288", "GSM3378289", "GSM3378290", "GSM3378291", "GSM3378292", "GSM3378293", "GSM3378294", "GSM3378295", "GSM3378296", "GSM3378297", "GSM3378298", "GSM3378299", "GSM3378300", "GSM3378301", "GSM3378302", "GSM3378303", "GSM3378304", "GSM3378305", "GSM3378306", "GSM3378307", "GSM3378308", "GSM3378309", "GSM3378310", "GSM3378311", "GSM3378312", "GSM3378313", "GSM3378314", "GSM3378315", "GSM3378316", "GSM3378317", "GSM3378318", "GSM3378319", "GSM3378320", "GSM3378321", "GSM3378322", "GSM3378323", "GSM3378324", "GSM3378325", "GSM3378326", "GSM3378327", "GSM3378328", "GSM3378329", "GSM3378330", "GSM3378331", "GSM3378332", "GSM3378333", "GSM3378334", "GSM3378335", "GSM3378336", "GSM3378337", "GSM3378338", "GSM3378339", "GSM3378340", "GSM3378341", "GSM3378342", "GSM3378343", "GSM3378344", "GSM3378345", "GSM3378346", "GSM3378347", "GSM3378348", "GSM3378349", "GSM3378350", "GSM3378351", "GSM3378352", "GSM3378353", "GSM3378354", "GSM3378355", "GSM3378356", "GSM3378357", "GSM3378358", "GSM3378359", "GSM3378360", "GSM3378361", "GSM3378362", "GSM3378363", "GSM3378364", "GSM3378365", "GSM3378366", "GSM3378367", "GSM3378368", "GSM3378369", "GSM3378370", "GSM3378371", "GSM3378372", "GSM3378373", "GSM3378374", "GSM3378375", "GSM3378376", "GSM3378377", "GSM3378378", "GSM3378379", "GSM3378380", "GSM3378381", "GSM3378382", "GSM3378383", "GSM3378384", "GSM3378385", "GSM3378386", "GSM3378387", "GSM3378388", "GSM3378389", "GSM3378390", "GSM3378391", "GSM3378392", "GSM3378393", "GSM3378394", "GSM3378395", "GSM3378396", "GSM3378397", "GSM3378398", "GSM3378399", "GSM3378400", "GSM3378401", "GSM3378402", "GSM3378403", "GSM3378404", "GSM3378405", "GSM3378406", "GSM3378407", "GSM3378408", "GSM3378409", "GSM3378410", "GSM3378411", "GSM3378412", "GSM3378413", "GSM3378414", "GSM3378415", "GSM3378416", "GSM3378417", "GSM3378418", "GSM3378419", "GSM3378420", "GSM3378421", "GSM3378422", "GSM3378423", "GSM3378424", "GSM3378425", "GSM3378426", "GSM3378427", "GSM3378428", "GSM3378429", "GSM3378430", "GSM3378431", "GSM3378432", "GSM3378433", "GSM3378434", "GSM3378435", "GSM3378436", "GSM3378437", "GSM3378438", "GSM3378439", "GSM3378440", "GSM3378441", "GSM3378442", "GSM3378443", "GSM3378444", "GSM3378445", "GSM3378446", "GSM3378447", "GSM3378448", "GSM3378449", "GSM3378450", "GSM3378451", "GSM3378452", "GSM3378453", "GSM3378454", "GSM3378455", "GSM3378456", "GSM3378457", "GSM3378458", "GSM3378459", "GSM3378460", "GSM3378461", "GSM3378462", "GSM3378463", "GSM3378464", "GSM3378465", "GSM3378466", "GSM3378467", "GSM3378468", "GSM3378469", "GSM3378470", "GSM3378471", "GSM3378472", "GSM3378473", "GSM3378474", "GSM3378475", "GSM3378476", "GSM3378477", "GSM3378478", "GSM3378479", "GSM3378480", "GSM3378481", "GSM3378482", "GSM3378483", "GSM3378484", "GSM3378485", "GSM3378486", "GSM3378487", "GSM3378488", "GSM3378489", "GSM3378490", "GSM3378491", "GSM3378492", "GSM3378493", "GSM3378494", "GSM3378495", "GSM3378496", "GSM3378497", "GSM3378498", "GSM3378499", "GSM3378500", "GSM3378501", "GSM3378502", "GSM3378503", "GSM3378504", "GSM3378505", "GSM3378506", "GSM3378507", "GSM3378508"], "sample_count": 370, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Common functional alterations identified in blood transcriptome of autoimmune cholestatic liver and inflammatory bowel diseases", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE119600 not downloaded", "asset:data:geo:GSE119600 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "genetic_association", "specific": "mendelian_randomisation", "label": "Genetic association (GWAS / linkage / MR)", "dsl_operations": ["mr_estimate"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["genotype_phenotype_table"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Two-sample Mendelian randomization analysis was conducted using the TwoSampleMR package [29]."}}], "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": ["mr_estimate"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mendelian_randomisation."}, "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": ["GSE119600"], "resolved_accessions": ["GSE119600"], "statements": ["The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s. All data and original files in our work are freely available under a ‘Creative Commons BY 4.0’ license. All methods were carried out in accordance with relevant guidelines and regulations."], "basis": "The paper names GSE119600 in Gene Expression Omnibus (GEO) repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["mr_estimate"], "assets": ["source:pmid:38809509", "data:geo:GSE119600"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE119600"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:19:54Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11249, "completion_tokens": 2073, "cached_tokens": 264}}, "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:38809509", "type": "paper", "label": "pmid:38809509"}, {"id": "source:pmid:38809509", "type": "manuscript", "label": "PMID 38809509 full text"}, {"id": "data:geo:GSE119600", "type": "dataset", "label": "GEO GSE119600"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38809509", "type": "paper", "label": "pmid:38809509"}, {"id": "source:pmid:38809509", "type": "manuscript", "label": "PMID 38809509 full text"}, {"id": "data:geo:GSE119600", "type": "dataset", "label": "GEO GSE119600"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38809509", "type": "extraction", "used": ["source:pmid:38809509"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE119600", "type": "accession_resolution", "used": ["data:geo:GSE119600"], "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:38809509", "parent_hash": "sha256:c2863fe1a3b63d33d62d0e3a99189d22174e63201314c8dbc3fbc44ba32a69dc", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE119600 licence not read", "asset:data:geo:GSE119600 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "genetic_association", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["mr_estimate"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Two-sample Mendelian randomization analysis was conducted using the TwoSampleMR package [29]."], "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":"2026-11-04T02:15:46+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}}}