{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38520027", "kind": "science-record", "revision": 3, "content_hash": "sha256:568d18579794f07f1e3f5526c3e351c4c10b6477715ba0abbb69974fb45971ba", "created_at": "2026-11-01T19:20:27Z", "updated_at": "2026-11-01T21:32:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential biomarkers for aging diagnosis of mesenchymal stem cells derived from the aged donors.", "doi": "10.1186/s13287-024-03689-1", "pmid": "38520027", "authors": ["Miao Hao", "Hongyu Jiang", "Yuan Zhao", "Chunyi Li", "Jinlan Jiang"], "journal": "Stem cell research & therapy", "year": 2024, "abstract": "BACKGROUND: The clinical application of human bone-marrow derived mesenchymal stem cells (MSCs) for the treatment of refractory diseases has achieved remarkable results. However, there is a need for a systematic evaluation of the quality and safety of MSCs sourced from donors. In this study, we sought to assess one potential factor that might impact quality, namely the age of the donor.\nMETHODS: We downloaded two data sets from each of two Gene Expression Omnibus (GEO), GSE39035 and GSE97311 databases, namely samples form young (< 65 years of age) and old (> 65) donor groups. Through, bioinformatics analysis and experimental validation to these retrieved data, we found that MSCs derived from aged donors can lead to differential expression of gene profiles compared with those from young donors, and potentially affect the function of MSCs, and may even induce malignant tumors.\nRESULTS: We identified a total of 337 differentially expressed genes (DEGs), including two upregulated and eight downregulated genes from the databases of both GSE39035 and GSE97311. We further identified 13 hub genes. Six of them, TBX15, IGF1, GATA2, PITX2, SNAI1 and VCAN, were highly expressed in many human malignancies in Human Protein Atlas database. In the MSCs in vitro senescent cell model, qPCR analysis validated that all six hub genes were highly expressed in senescent MSCs. Our findings confirm that aged donors of MSCs have a significant effect on gene expression profiles. The MSCs from old donors have the potential to cause a variety of malignancies. These TBX15, IGF1, GATA2, PITX2, SNAI1, VCAN genes could be used as potential biomarkers to diagnosis aging state of donor MSCs, and evaluate whether MSCs derived from an aged donor could be used for therapy in the clinic. Our findings provide a diagnostic basis for the clinical use of MSCs to treat a variety of diseases.\nCONCLUSIONS: Therefore, our findings not only provide guidance for the safe and standardized use of MSCs in the clinic for the treatment of various diseases, but also provide insights into the use of cell regeneration approaches to reverse aging and support rejuvenation.", "claims": [{"id": "claim-method", "statement": "Using SPSS 22.0, we constructed receiver operating characteristic (ROC) curves and calculated the area under the curve (AUC) of the hub genes to compare the AUC as the index of the model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38520027", "locator": "sections[13] \"Statistics analysis\" paragraph 2", "quote": "Using SPSS 22.0, we constructed receiver operating characteristic (ROC) curves and calculated the area under the curve (AUC) of the hub genes to compare the AUC as the index of the model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed in this study are available in GEO database. GSE39035 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39035. GSE97311 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97311.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38520027", "locator": "sections[28] \"Data availability\" paragraph 2", "quote": "The datasets analyzed in this study are available in GEO database. GSE39035 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39035. GSE97311 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97311."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Receiver operating characteristic curve analysis of two public GEO microarray datasets identified TBX15, IGF1, GATA2, PITX2, SNAI1, and VCAN as potential biomarkers of MSC donor age.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Figure 5A shows the results of GSE39035: the AUC for TBX15, IGF1, GATA2, PITX2, SNAI1, VCAN were 1.000 [95% confidence interval (Cl), 1.000–1.000; P < 0.05], 0.938 (95% Cl, 0.824-1.000; P < 0.05), 0.750 (95% Cl, 0.488-1.000; P < 0.05), 1.000 (95% Cl, 1.000–1.000; P < 0.05), 0.891 (95% Cl, 0.700-1.000; P < 0.05) and 0.984 (95% Cl, 0.941-1.000; P < 0.05)."}, "evidence": [{"asset": "source:pmid:38520027", "locator": "sections[19] \"Validation of diagnostic value of hub genes\" paragraph 2", "quote": "These results indicate that TBX15, IGF1, GATA2, PITX2 SNAI1 and VCAN may serve as potential biomarkers for evaluating the age of MSCs donors or the quality of MSCs."}, {"asset": "source:pmid:38520027", "locator": "sections[19] \"Validation of diagnostic value of hub genes\" paragraph 2", "quote": "Figure 5A shows the results of GSE39035: the AUC for TBX15, IGF1, GATA2, PITX2, SNAI1, VCAN were 1.000 [95% confidence interval (Cl), 1.000–1.000; P < 0.05], 0.938 (95% Cl, 0.824-1.000; P < 0.05), 0.750 (95% Cl, 0.488-1.000; P < 0.05), 1.000 (95% Cl, 1.000–1.000; P < 0.05), 0.891 (95% Cl, 0.700-1.000; P < 0.05) and 0.984 (95% Cl, 0.941-1.000; P < 0.05)."}, {"asset": "source:pmid:38520027", "locator": "sections[19] \"Validation of diagnostic value of hub genes\" paragraph 2", "quote": "Figure 5B shows the AUC curve in the groups classified as young and old in the GSE97311 datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Receiver operating characteristic curve analysis of two public GEO microarray datasets identified TBX15, IGF1, GATA2, PITX2, SNAI1, and VCAN as potential biomarkers of MSC donor age.", "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:38520027"], "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:GSE39035"], "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:GSE39035"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38520027", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13287-024-03689-1", "sha256": "sha256:e477250d6af69f8b631568341956526da259869a293363ecdb4d9155d8597925", "bytes": 46419, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13287-024-03689-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10960456", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE39035", "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=GSE39035", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39035", "version": null, "note": "The datasets analyzed in this study are available in GEO database. GSE39035 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39035. GSE97311 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97311.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed in this study are available in GEO database. GSE39035 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39035. 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GSE39035 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39035. GSE97311 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97311.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed in this study are available in GEO database. GSE39035 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39035. GSE97311 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97311.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2561499", "GSM2561500", "GSM2561501", "GSM2561502", "GSM2561503", "GSM2561504", "GSM2561505", "GSM2561506", "GSM2561507", "GSM2561508", "GSM2561509", "GSM2561510", "GSM2561511", "GSM2561512", "GSM2561513", "GSM2561514", "GSM2561515", "GSM2561516"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Induced Mesenchymal stromal cells derived from iPS cells from aged individuals acquire a rejuvenation signature and a MSC-specific secretome", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE39035 not downloaded", "asset:data:geo:GSE39035 licence not read", "asset:data:geo:GSE97311 not downloaded", "asset:data:geo:GSE97311 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Receiver operating characteristic (ROC) curve analysis with area under the curve (AUC)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Using SPSS 22.0, we constructed receiver operating characteristic (ROC) curves and calculated the area under the curve (AUC) of the hub genes to compare the AUC as the index of the model."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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 (Receiver operating characteristic (ROC) curve analysis with area under the curve (AUC)), 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": ["GSE39035", "GSE97311"], "resolved_accessions": ["GSE39035", "GSE97311"], "statements": ["The datasets analyzed in this study are available in GEO database. GSE39035 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39035. GSE97311 repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97311."], "basis": "The paper names GSE39035, GSE97311 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:38520027", "data:geo:GSE39035"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE39035"]}, "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": "2026-11-01T19:13:09Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14169, "completion_tokens": 1833, "cached_tokens": 128}}, "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:38520027", "type": "paper", "label": "pmid:38520027"}, {"id": "source:pmid:38520027", "type": "manuscript", "label": "PMID 38520027 full text"}, {"id": "data:geo:GSE39035", "type": "dataset", "label": "GEO GSE39035"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38520027", "type": "paper", "label": "pmid:38520027"}, {"id": "source:pmid:38520027", "type": "manuscript", "label": "PMID 38520027 full text"}, {"id": "data:geo:GSE39035", "type": "dataset", "label": "GEO GSE39035"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38520027", "type": "extraction", "used": ["source:pmid:38520027"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE39035", "type": "accession_resolution", "used": ["data:geo:GSE39035"], "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:38520027", "parent_hash": "sha256:1fd0636037a9ab5a896548a375abf98fbf731385e9af28b645db3788a1437e68", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE39035 licence not read", "asset:data:geo:GSE39035 not downloaded", "asset:data:geo:GSE97311 licence not read", "asset:data:geo:GSE97311 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": [". In the MSCs in vitro senescent cell model, qPCR analysis validated that all six hub genes we"], "order_basis": "paper_text_order:1358", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ale) were purchased from OriCell®. MSCs were cultured in basal medium supplemented with 10% fetal bov"], "order_basis": "paper_text_order:2359", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:32:26+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}}}