{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31372048", "kind": "science-record", "revision": 9, "content_hash": "sha256:740303c97c45c28e3b3f3f7eb2388c26e9d4f8bfe49914cbcf78e62d8a178151", "created_at": "2026-11-01T15:40:48Z", "updated_at": "2026-11-01T22:44:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "FGF5 promotes osteosarcoma cells proliferation via activating MAPK signaling pathway.", "doi": "10.2147/CMAR.S200234", "pmid": "31372048", "authors": ["Dunxin Han", "Mingming Wang", "Zhongkai Yu", "Long Yin", "Changli Liu", "Jianmin Wang", "Yongjun Liu", "Shengyang Jiang", "Zhongwu Ren", "Jun Yin"], "journal": "Cancer management and research", "year": 2019, "abstract": "Objective: This study aimed to investigate the role of fibroblast growth factor-5 (FGF5) in osteosarcoma (OS) and explore the potential mechanisms. Methods: OS gene expression data was downloaded from the Gene Expression Omnibus (GEO; GSE12865) and analyzed by R software. OS tissues and cell lines were collected. The expression level of FGF5 in tumor tissues and cell lines was detected using qRT-PCR. Knockout of FGF5 was performed using CRISPR/Cas9 system. The effects of FGF5 knockout on OS cell proliferation and tumor growth were determined through cell counting kit-8 assay and xenograft nude mice, respectively. Additionally, recombinant FGF5 (rFGF5) was added into OS cell and the effects of rFGF5 on the proliferation and apoptosis of OS cell lines were assayed. Furthermore, the protein expression levels of mitogen-activated protein kinase (MAPK) signaling pathway were detected through Western blot. Results: FGF5 was significantly upregulated in OS tissues and cells, and closely associated with poor differentiation, larger tumor size, lymph node metastasis, and advanced TNM stage. FGF5 knockout could inhibit proliferation of OS cells and tumor growth in nude mouse model. Addition of exogenous rFGF5 promoted OS cell proliferation while inhibited OS cell apoptosis. The expression levels of MAPK signaling pathway proteins in FGF5 knockout group were significantly lower than that in control when there was no rFGF5. Additionally, their expression level in rFGF5 addition group was higher than that in without rFGF5 group. Conclusion: We demonstrated for the first time that FGF5 was overexpressed in OS cell lines and clinical tissue samples and promotes OS cell proliferation by activating MAPK signaling pathway, which indicated that FGF5 was a potential therapeutic target for OS.", "claims": [{"id": "claim-method", "statement": "The P-values were calculated using a one-way ANOVA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31372048", "locator": "sections[14] \"Statistical analysis\" paragraph 2", "quote": "The P-values were calculated using a one-way ANOVA."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The expression profiling data (accession number: GSE12865) deposited in Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/) were extracted for analysis. The dataset included two replications of normal human osteoblasts and 12 osteosarcoma tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31372048", "locator": "sections[8] \"Expression profiling data collection and differential expression analysis\" paragraph 2", "quote": "The expression profiling data (accession number: GSE12865) deposited in Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/) were extracted for analysis. The dataset included two replications of normal human osteoblasts and 12 osteosarcoma tissues."}], "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:31372048"], "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:GSE12865"], "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:GSE12865"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31372048", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/CMAR.S200234", "sha256": "sha256:79e50a6e4a8c33314b83d63dbab37fe7fbe7572e7210ec846d414c80ab1faeb0", "bytes": 30177, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/CMAR.S200234", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6628182", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12865", "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=GSE12865", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12865", "version": null, "note": "The expression profiling data (accession number: GSE12865) deposited in Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/) were extracted for analysis. The dataset included two replications of normal human osteoblasts and 12 osteosarcoma tissues.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The expression profiling data (accession number: GSE12865) deposited in Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/) were extracted for analysis. The dataset included two replications of normal human osteoblasts and 12 osteosarcoma tissues.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM288005", "GSM288006", "GSM322691", "GSM322692", "GSM322693", "GSM322694", "GSM322695", "GSM322696", "GSM322697", "GSM322698", "GSM322699", "GSM322700", "GSM322701", "GSM322702"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression of human paediatric osteosarcoma tumour samples relative to normal human osteoblasts", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31372048:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:089f5aacb56627f3569de878aadd191b6c0caa6b308e5553867ced1f0f7483c6", "bytes": 1208, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T0001", "version": null, "note": "Correlation between FGF5 expression and clinical-pathological characteristic in 15 osteosarcoma patients", "structure": {"pmcid": "PMC6628182", "section_index": 16, "section_title": "FGF5 was upregulated in OS", "row_count": 31, "column_count": 5}, "table": {"label": "Table 1", "caption": "Correlation between FGF5 expression and clinical-pathological characteristic in 15 osteosarcoma patients", "rows": [["", "", "FGF5 expression", ""], ["Characteristics", "Case number", "Low", "High", "P-value"], ["Gender", "", "", "", ""], ["Male", "9", "4", "6", "0.706"], ["Female", "6", "2", "3", ""], ["Age", "", "", "", ""], ["≤25", "12", "6", "6", "0.185"], ["25", "3", "0", "3", ""], ["Tumor location", "", "", "", ""], ["Tibia/femur", "10", "4", "6", "0.706"], ["Elsewhere", "5", "2", "3", ""], ["Histology types", "", "", "", ""], ["Osteoblast type", "8", "5", "3", ""], ["Chondroblast type", "4", "2", "2", "0.467"], ["Other type", "3", "1", "2", ""], ["X-ray types", "", "", "", ""], ["Osteogenesis type", "5", "3", "2", ""], ["Osteolysis type", "7", "3", "4", "0.35"], ["Mixed type", "3", "1", "2", ""], ["Differentiated degree", "", "", "", ""], ["High", "9", "2", "7", "0.035"], ["Low", "6", "5", "1", ""], ["Tumor size", "", "", "", ""], ["8 cm", "5", "4", "1", "0.047"], ["8 cm", "10", "2", "8", ""], ["Lymph node metastasis", "", "", "", ""], ["Yes", "11", "2", "9", "0.011"], ["No", "4", "4", "0", ""], ["Tumor stage", "", "", "", ""], ["IIA", "26", "3", "0", "0.044"], ["IIB/III", "34", "3", "9", ""]], "row_count": 31, "column_count": 5, "numeric_cells": 73, "header_rows": 2, "locator": "section[16]/table-wrap[1]#T0001"}}], "gaps": ["asset:data:geo:GSE12865 not downloaded", "asset:data:geo:GSE12865 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The P-values were calculated using a one-way ANOVA."}}], "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["GSE12865"], "resolved_accessions": ["GSE12865"], "statements": ["The expression profiling data (accession number: GSE12865) deposited in Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/) were extracted for analysis. The dataset included two replications of normal human osteoblasts and 12 osteosarcoma tissues."], "basis": "The paper names GSE12865 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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:31372048", "data:geo:GSE12865", "asset:table:pmid:31372048:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12865"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:35Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 24664, "completion_tokens": 696, "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:31372048", "type": "paper", "label": "pmid:31372048"}, {"id": "source:pmid:31372048", "type": "manuscript", "label": "PMID 31372048 full text"}, {"id": "data:geo:GSE12865", "type": "dataset", "label": "GEO GSE12865"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31372048", "type": "paper", "label": "pmid:31372048"}, {"id": "source:pmid:31372048", "type": "manuscript", "label": "PMID 31372048 full text"}, {"id": "data:geo:GSE12865", "type": "dataset", "label": "GEO GSE12865"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31372048", "type": "extraction", "used": ["source:pmid:31372048"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12865", "type": "accession_resolution", "used": ["data:geo:GSE12865"], "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:31372048", "parent_hash": "sha256:f673d0c31bbbed0dfa4fe2af2603badfae3fd24bdf5179334c746c9a495a8131", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE12865 licence not read", "asset:data:geo:GSE12865 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["RT-PCR. Knockout of FGF5 was performed using CRISPR/Cas9 system. The effects of FGF5 knockout on"], "order_basis": "paper_text_order:482", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["he effects of rFGF5 on the proliferation and apoptosis of OS cell lines were assayed. Furthermore,", "S cell proliferation while inhibited OS cell apoptosis. The expression levels of MAPK signaling pat"], "order_basis": "paper_text_order:774", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["APK) signaling pathway were detected through Western blot. Results: FGF5 was significantly upregulated"], "order_basis": "paper_text_order:941", "id": "assay:3"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["eration of OS cells and tumor growth in nude mouse model. Addition of exogenous rFGF5 promoted OS cel", "eration of OS cells and tumor growth in nude mouse model. Addition of exogenous rFGF5 promoted"], "order_basis": "paper_text_order:1219", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["(Shanghai, China). HOBC and NHOST cells were cultured in DMEM/ham’s F-12 (Invitrogen, Carlsbad, CA, U", "ies, Grand Island, NY, USA). KHOS cells were cultured in RPMI 1640 medium (Invitrogen) supplemented w", "lls HOBC and NHOST, as well as OS cell lines U2OS, SAOS, MG63, and KHOS were purchased from th", "ning 10% FBS(Invitrogen) and 0.3 mg/ml G418. U2OS, MG63, and SAOS cells were maintained in DME"], "order_basis": "paper_text_order:2656", "id": "assay:5"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The P-values were calculated using a one-way ANOVA."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]},"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":"2026-11-04T01:34:37+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}}}