{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484191", "kind": "science-record", "revision": 6, "content_hash": "sha256:4802c4cba427701f80fe1b0d519f870592f8da89360bb8f33b5978431c34812c", "created_at": "2026-11-01T15:40:12Z", "updated_at": "2026-11-01T21:20:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiling of loss of TET2 and/or JAK2V617F mutant hematopoietic stem cells from mouse models of myeloproliferative neoplasms.", "doi": "10.1016/j.gdata.2015.04.002", "pmid": "26484191", "authors": ["Takuro Kameda", "Kotaro Shide", "Takumi Yamaji", "Ayako Kamiunten", "Masaaki Sekine", "Tomonori Hidaka", "Yoko Kubuki", "Goro Sashida", "Kazumasa Aoyama", "Makoto Yoshimitsu", "Hiroo Abe", "Tadashi Miike", "Hisayoshi Iwakiri", "Yoshihiro Tahara", "Shojiro Yamamoto", "Satoru Hasuike", "Kenji Nagata", "Atsushi Iwama", "Akira Kitanaka", "Kazuya Shimoda"], "journal": "Genomics data", "year": 2015, "abstract": "Myeloproliferative neoplasms (MPNs) are clinically characterized by the chronic overproduction of differentiated peripheral blood cells and the gradual expansion of malignant intramedullary/extramedullary hematopoiesis. In MPNs mutations in JAK2 MPL or CALR are detected mutually exclusive in more than 90% of cases [1,2]. Mutations in them lead to the abnormal activation of JAK/STAT signaling and the autonomous growth of differentiated cells therefore they are considered as \"driver\" gene mutations. In addition to the above driver gene mutations mutations in epigenetic regulators such as TET2 DNMT3A ASXL1 EZH2 or IDH1/2 are detected in about 5%-30% of cases respectively [3]. Mutations in TET2 DNMT3A EZH2 or IDH1/2 commonly confer the increased self-renewal capacity on normal hematopoietic stem cells (HSCs) but they do not lead to the autonomous growth of differentiated cells and only exhibit subtle clinical phenotypes [4,6-8,5]. It was unclear how mutations in such epigenetic regulators influenced abnormal HSCs with driver gene mutations how they influenced the disease phenotype or whether a single driver gene mutation was sufficient for the initiation of human MPNs. Therefore we focused on JAK2V617F and loss of TET2-the former as a representative of driver gene mutations and the latter as a representative of mutations in epigenetic regulators-and examined the influence of single or double mutations on HSCs (Lineage(-)Sca-1(+)c-Kit(+) cells (LSKs)) by functional analyses and microarray whole-genome expression analyses [9]. Gene expression profiling showed that the HSC fingerprint genes [10] was statistically equally enriched in TET2-knockdown-LSKs but negatively enriched in JAK2V617F-LSKs compared to that in wild-type-LSKs. Double-mutant-LSKs showed the same tendency as JAK2V617F-LSKs in terms of their HSC fingerprint genes but the expression of individual genes differed between the two groups. Among 245 HSC fingerprint genes 100 were more highly expressed in double-mutant-LSKs than in JAK2V617F-LSKs. These altered gene expressions might partly explain the mechanisms of initiation and progression of MPNs which was observed in the functional analyses [9]. Here we describe gene expression profiles deposited at the Gene Expression Omnibus (GEO) under the accession number GSE62302 including experimental methods and quality control analyses.", "claims": [{"id": "claim-method", "statement": "Gene set enrichment analysis (GSEA) [12] was performed across the complete list of genes ranked by signal-to-noise ratio according to their differential expression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484191", "locator": "sections[13] \"Data analysis (gene set enrichment analysis (GSEA))\" paragraph 2", "quote": "Gene set enrichment analysis (GSEA) [12] was performed across the complete list of genes ranked by signal-to-noise ratio according to their differential expression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Here we describe gene expression profiles deposited at the Gene Expression Omnibus (GEO) under the accession number GSE62302 including experimental methods and quality control analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484191", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we describe gene expression profiles deposited at the Gene Expression Omnibus (GEO) under the accession number GSE62302 including experimental methods and quality control analyses."}], "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:26484191"], "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:GSE62302"], "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:GSE62302"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484191", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.04.002", "sha256": "sha256:c9be3eee30977dc7c94a325f8f81b7e7cbe9e0f6f4c6e8cd7a1f45e199f0ff71", "bytes": 20500, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.04.002", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4535894", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62302", "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=GSE62302", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62302", "version": null, "note": "Here we describe gene expression profiles deposited at the Gene Expression Omnibus (GEO) under the accession number GSE62302 including experimental methods and quality control analyses.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Here we describe gene expression profiles deposited at the Gene Expression Omnibus (GEO) under the accession number GSE62302 including experimental methods and quality control analyses.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1525032", "GSM1525033", "GSM1525034", "GSM1525035"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "10787", "taxon": "Mus musculus", "title": "Expression data from loss-of-TET2 and/or JAK2V617F mutant Lineage-c-Kit+Sca-1+ (LSK) bone marrow cells", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26484191:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:954ef444a6298efa6ff2f771b10c0ed8c8395b6115ae943b27a1286a8615f0c0", "bytes": 441, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#t0005", "version": null, "note": "Four experimental groups defined by the JAK2-and-TET2 mutation status of the experimental tissues or cells.", "structure": {"pmcid": "PMC4535894", "section_index": 4, "section_title": "Mouse usage", "row_count": 5, "column_count": 3}, "table": {"label": "Table 1", "caption": "Four experimental groups defined by the JAK2-and-TET2 mutation status of the experimental tissues or cells.", "rows": [["Annotation", "JAK2 status", "TET2 status"], ["WT", "JAK2WT", "TET2WT"], ["TET2KD", "JAK2WT", "TET2trap/trap"], ["JAK2V617F", "JAK2V617F", "TET2WT"], ["Double-mutant", "JAK2V617F", "TET2trap/trap"]], "row_count": 5, "column_count": 3, "numeric_cells": 3, "header_rows": 1, "locator": "section[4]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:26484191:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b0afa11653ed621efd85c9ec75c4e0cbb31b2fc75e7b21f8f0696fef48d46df4", "bytes": 3996, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t0010", "version": null, "note": "HSC fingerprint genes expressed more highly in double mutant-LSKs than in JAK2V617F–LSKs.For each HSC fingerprint gene, Agilent probe ID, RefSeq ID, normalized expression values (log2) in each mutant LSKs and the value of the log2 fold change (log2FC) (Double mutant vs. JAK2V617F) are shown. HSC fingerprint genes are arranged in descending order of the value of the log2FC.", "structure": {"pmcid": "PMC4535894", "section_index": 13, "section_title": "Data analysis (gene set enrichment analysis (GSEA))", "row_count": 38, "column_count": 8}, "table": {"label": "Table 2", "caption": "HSC fingerprint genes expressed more highly in double mutant-LSKs than in JAK2V617F–LSKs.For each HSC fingerprint gene, Agilent probe ID, RefSeq ID, normalized expression values (log2) in each mutant LSKs and the value of the log2 fold change (log2FC) (Double mutant vs. JAK2V617F) are shown. HSC fingerprint genes are arranged in descending order of the value of the log2FC.", "rows": [["Probe ID", "RefSeq ID", "Gene symbol", "WT", "TET2KD", "JAK2 V617F", "Double-mutant", "log2FC (double mutant vs. JAK2V617F)"], ["A_55_P2174935", "NM_001081235", "MN1", "0.230", "− 0.936", "− 5.367", "− 0.130", "5.237"], ["A_51_P469480", "NM_009535", "YES1", "− 4.917", "− 4.721", "− 4.618", "0.502", "5.120"], ["A_55_P2078710", "NM_029413", "MORC4", "2.775", "0.403", "− 4.103", "− 0.382", "3.721"], ["A_52_P17098", "NM_001161620", "MPP7", "− 2.307", "− 1.290", "− 2.043", "1.666", "3.709"], ["A_51_P384148", "NM_013649", "RYK", "− 5.134", "− 4.928", "− 5.348", "− 1.843", "3.505"], ["A_55_P2121985", "NM_013829", "PLCB4", "− 0.339", "− 0.537", "− 1.038", "2.245", "3.283"], ["A_65_P16750", "NM_001163609", "PSMA8", "− 4.958", "− 4.351", "− 4.187", "− 1.193", "2.994"], ["A_51_P501803", "NM_010451", "HOXA2", "− 3.562", "− 2.678", "− 5.015", "− 2.069", "2.946"], ["A_51_P258409", "NM_010423", "HEY1", "− 4.939", "− 1.361", "− 4.175", "− 1.249", "2.926"], ["A_52_P121342", "NM_020252", "NRXN1", "0.839", "1.021", "− 2.792", "0.010", "2.802"], ["A_55_P2129271", "NM_001285498", "TEAD2", "− 3.023", "− 1.465", "− 3.308", "− 0.683", "2.625"], ["A_55_P1955457", "NM_010345", "GRB10", "− 1.329", "− 1.564", "− 3.263", "− 0.660", "2.603"], ["A_51_P293781", "NM_016863", "FKBP1B", "− 4.324", "− 1.063", "− 3.222", "− 0.629", "2.593"], ["A_55_P2066463", "NM_010135", "ENAH", "− 5.220", "− 5.021", "− 4.031", "− 1.655", "2.376"], ["A_52_P162486", "NM_007542", "BGN", "0.864", "1.299", "− 5.224", "− 2.941", "2.283"], ["A_55_P1966644", "NM_013838", "TRPC6", "0.286", "− 1.267", "− 3.580", "− 1.300", "2.280"], ["A_51_P462102", "NM_133911", "GPR125", "− 4.796", "− 2.431", "− 2.045", "− 0.073", "1.972"], ["A_66_P136228", "NM_030690", "RAI14", "− 1.642", "1.334", "− 5.468", "− 3.539", "1.929"], ["A_66_P134991", "NM_028360", "TTC19", "− 3.783", "0.111", "− 1.617", "0.297", "1.914"], ["A_55_P1981155", "NM_153537", "PHLDB1", "− 3.791", "− 2.611", "− 5.050", "− 3.227", "1.822"], ["A_55_P2262136", "NM_013690", "TEK", "− 1.750", "− 2.354", "− 5.453", "− 3.726", "1.727"], ["A_55_P2154659", "NM_023651", "PEX13", "− 4.951", "− 4.765", "− 1.839", "− 0.187", "1.652"], ["A_51_P258493", "NM_011067", "PER3", "− 5.172", "− 2.979", "− 4.253", "− 2.680", "1.573"], ["A_66_P114381", "NM_001005341", "YPEL2", "0.865", "2.139", "− 2.649", "− 1.103", "1.547"], ["A_55_P2163319", "NM_008817", "PEG3", "− 5.166", "− 4.958", "− 5.380", "− 3.871", "1.510"], ["A_55_P2036026", "NM_028783", "ROBO4", "0.744", "0.297", "− 1.038", "0.469", "1.506"], ["A_55_P2137887", "NM_010820", "MPDZ", "− 5.192", "− 5.020", "− 5.454", "− 3.969", "1.485"], ["A_55_P2000758", "NM_019832", "GKAP1", "0.273", "0.416", "− 1.831", "− 0.398", "1.433"], ["A_51_P350453", "NM_013743", "PDK4", "− 3.333", "− 4.200", "− 5.482", "− 4.071", "1.410"], ["A_51_P463003", "NM_021367", "TSLP", "− 2.800", "− 4.719", "− 3.351", "− 2.000", "1.351"], ["A_55_P1968362", "NM_011599", "TLE1", "0.466", "1.850", "− 0.451", "0.865", "1.316"], ["A_55_P2038056", "NM_080285", "CTTNBP2", "− 4.706", "− 4.534", "− 5.502", "− 4.272", "1.230"], ["A_51_P361220", "NM_008055", "FZD4", "− 2.366", "− 1.957", "− 4.903", "− 3.674", "1.229"], ["A_51_P249930", "NM_146236", "TCEAL1", "− 5.003", "− 3.211", "− 3.418", "− 2.247", "1.171"], ["A_52_P20048", "NM_011544", "TCF12", "0.393", "− 1.130", "− 1.777", "− 0.661", "1.116"], ["A_55_P2092859", "NM_013471", "ANXA4", "2.783", "1.534", "− 0.644", "0.459", "1.103"], ["A_55_P2109559", "NM_001013616", "TRIM6", "− 2.055", "− 3.687", "− 3.141", "− 2.101", "1.041"]], "row_count": 38, "column_count": 8, "numeric_cells": 267, "header_rows": 1, "locator": "section[13]/table-wrap[1]#t0010"}}], "gaps": ["asset:data:geo:GSE62302 not downloaded", "asset:data:geo:GSE62302 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Gene set enrichment analysis (GSEA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Gene set enrichment analysis (GSEA) [12] was performed across the complete list of genes ranked by signal-to-noise ratio according to their differential expression."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Gene set enrichment analysis (GSEA)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE62302"], "resolved_accessions": ["GSE62302"], "statements": ["Here we describe gene expression profiles deposited at the Gene Expression Omnibus (GEO) under the accession number GSE62302 including experimental methods and quality control analyses."], "basis": "The paper names GSE62302 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26484191", "data:geo:GSE62302", "asset:table:pmid:26484191:1", "asset:table:pmid:26484191:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE62302"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:06:16Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 18835, "completion_tokens": 1117, "cached_tokens": 648}}, "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:26484191", "type": "paper", "label": "pmid:26484191"}, {"id": "source:pmid:26484191", "type": "manuscript", "label": "PMID 26484191 full text"}, {"id": "data:geo:GSE62302", "type": "dataset", "label": "GEO GSE62302"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484191", "type": "paper", "label": "pmid:26484191"}, {"id": "source:pmid:26484191", "type": "manuscript", "label": "PMID 26484191 full text"}, {"id": "data:geo:GSE62302", "type": "dataset", "label": "GEO GSE62302"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484191", "type": "extraction", "used": ["source:pmid:26484191"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE62302", "type": "accession_resolution", "used": ["data:geo:GSE62302"], "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:26484191", "parent_hash": "sha256:a328764d78f17d9bf6362a17556c4b1c1145db8d78bf244257a9ecbc19109969", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE62302 licence not read", "asset:data:geo:GSE62302 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["K2V617F mutant hematopoietic stem cells from mouse models of myeloproliferative neoplasms."], "order_basis": "paper_text_order:51", "id": "assay:1"}, {"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": ["(+) cells (LSKs)) by functional analyses and microarray whole-genome expression analyses [9]. Gene e", "Experimental design, materials and methods Microarray study design Using the 4 experimental groups", "oups of prepared cDNA samples (each, n = 1), microarray gene expression analyses were performed. Eac"], "order_basis": "paper_text_order:1595", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["] was statistically equally enriched in TET2-knockdown-LSKs but negatively enriched in JAK2V617F-LS"], "order_basis": "paper_text_order:1756", "id": "assay:3"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T03:12:15+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}}}