{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25181531", "kind": "science-record", "revision": 8, "content_hash": "sha256:66378912c9dc9c01935a0042f63d7cb648a75166d2d8dab016d9a8c2f20b40bf", "created_at": "2026-11-01T15:40:05Z", "updated_at": "2026-11-01T22:42:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "RTCGAToolbox: a new tool for exporting TCGA Firehose data.", "doi": "10.1371/journal.pone.0106397", "pmid": "25181531", "authors": ["Mehmet Kemal Samur"], "journal": "PloS one", "year": 2014, "abstract": "BACKGROUND & OBJECTIVE: Managing data from large-scale projects (such as The Cancer Genome Atlas (TCGA)) for further analysis is an important and time consuming step for research projects. Several efforts, such as the Firehose project, make TCGA pre-processed data publicly available via web services and data portals, but this information must be managed, downloaded and prepared for subsequent steps. We have developed an open source and extensible R based data client for pre-processed data from the Firehouse, and demonstrate its use with sample case studies. Results show that our RTCGAToolbox can facilitate data management for researchers interested in working with TCGA data. The RTCGAToolbox can also be integrated with other analysis pipelines for further data processing.\nAVAILABILITY AND IMPLEMENTATION: The RTCGAToolbox is open-source and licensed under the GNU General Public License Version 2.0. All documentation and source code for RTCGAToolbox is freely available at http://mksamur.github.io/RTCGAToolbox/ for Linux and Mac OS X operating systems.", "claims": [{"id": "claim-method", "statement": "It takes sample barcodes to differentiate between “Normal” and “Tumor” samples, and compares them with linear models and empirical Bayesian methods provided by the limma [20] package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25181531", "locator": "sections[5] \"RTCGAToolbox Data Client and Analysis Functions\" paragraph 6", "quote": "It takes sample barcodes to differentiate between “Normal” and “Tumor” samples, and compares them with linear models and empirical Bayesian methods provided by the limma [20] package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors confirm that all data underlying the findings are fully available without restriction. 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All relevant data are within the paper and its Supporting Information files and http://mksamur.github.io/RTCGAToolbox."}], "state": "complete"}, {"id": "claim-target-result", "statement": "RTCGAToolbox facilitates management and downstream analysis of TCGA data accessed through the Firehose pre-processed data service, with differential gene-expression analysis implemented using limma linear models, empirical Bayesian methods, and voom.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25181531", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Results show that our RTCGAToolbox can facilitate data management for researchers interested in working with TCGA data."}, {"asset": "source:pmid:25181531", "locator": "sections[2] \"Implementation\" paragraph 4", "quote": "RTCGAToolbox uses the Firehose project, one of the largest TCGA data sources operated by Broad Institute's Genome Data Analysis Center (GDAC), to access Level 3 (segmented or interpreted data) and Level 4 (region of interest data) pre-processed data."}, {"asset": "source:pmid:25181531", "locator": "sections[2] \"Implementation\" paragraph 5", "quote": "The main module of the RTCGAToolbox accesses reports via HTTP calls, and uses text processing functionalities to prepare required information for subsequent steps."}, {"asset": "source:pmid:25181531", "locator": "sections[5] \"RTCGAToolbox Data Client and Analysis Functions\" paragraph 6", "quote": "The “getDiffExpressedGenes” function provides the results of differential gene expression analysis. It takes sample barcodes to differentiate between “Normal” and “Tumor” samples, and compares them with linear models and empirical Bayesian methods provided by the limma [20] package. It also uses voom [21] function (from the same package) to prepare raw RNAseq counts for differential gene expression analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "RTCGAToolbox facilitates management and downstream analysis of TCGA data accessed through the Firehose pre-processed data service, with differential gene-expression analysis implemented using limma linear models, empirical Bayesian methods, and voom.", "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:25181531"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25181531", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0106397", "sha256": "sha256:2843485a6da731605946b11c606cd401ee9cfb13d809e42b624b093b5154a887", "bytes": 25546, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0106397", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4152273", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:25181531:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43020e4b5de265e6ac067ca953f07273a5863d06bc9835846a2c94b80b2d991e", "bytes": 2245, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#pone-0106397-t001", "version": null, "note": "Current Firehose data content (Some of these data may not be accessible due to TCGA data restrictions, full data table can be accessible via http://gdac.broadinstitute.org/runs/stddata__2014_03_16/ingested_data.html).", "structure": {"pmcid": "PMC4152273", "section_index": 1, "section_title": "Introduction", "row_count": 32, "column_count": 10}, "table": {"label": "Table 1", "caption": "Current Firehose data content (Some of these data may not be accessible due to TCGA data restrictions, full data table can be accessible via http://gdac.broadinstitute.org/runs/stddata__2014_03_16/ingested_data.html).", "rows": [["Cohort", "Clinical", "CN", "Methylation", "mRNA", "mRNASeq", "miR", "miRSeq", "RPPA", "MAF"], ["ACC", "15", "90", "80", "0", "79", "0", "80", "0", "90"], ["BLCA", "198", "252", "242", "0", "241", "0", "241", "127", "130"], ["BRCA", "981", "1041", "1024", "526", "1037", "0", "1021", "408", "976"], ["CESC", "127", "192", "189", "0", "185", "0", "200", "0", "39"], ["COAD", "436", "427", "434", "153", "432", "0", "406", "331", "154"], ["COADREAD", "604", "589", "596", "222", "595", "0", "549", "461", "223"], ["DLBC", "21", "28", "28", "0", "28", "0", "27", "0", "0"], ["ESCA", "39", "97", "93", "0", "0", "0", "72", "0", "0"], ["GBM", "578", "570", "414", "540", "160", "565", "0", "214", "290"], ["HNSC", "408", "509", "457", "0", "497", "0", "512", "212", "306"], ["KICH", "93", "66", "66", "0", "66", "0", "66", "0", "66"], ["KIRC", "507", "514", "511", "72", "518", "0", "502", "454", "417"], ["KIRP", "164", "182", "198", "16", "172", "0", "198", "0", "168"], ["LAML", "200", "197", "194", "0", "179", "0", "188", "0", "197"], ["LGG", "305", "463", "403", "27", "463", "0", "438", "258", "289"], ["LIHC", "151", "190", "194", "0", "191", "0", "200", "0", "0"], ["LUAD", "466", "493", "555", "32", "488", "0", "491", "237", "229"], ["LUSC", "411", "490", "492", "154", "489", "0", "467", "195", "178"], ["MESO", "13", "37", "37", "0", "0", "0", "0", "0", "0"], ["OV", "580", "576", "584", "574", "296", "570", "453", "412", "316"], ["PAAD", "73", "91", "91", "0", "85", "0", "85", "0", "91"], ["PCPG", "10", "0", "179", "0", "0", "0", "0", "0", "0"], ["PRAD", "199", "331", "336", "0", "297", "0", "326", "164", "261"], ["READ", "168", "162", "162", "69", "163", "0", "143", "130", "69"], ["SARC", "102", "137", "170", "0", "103", "0", "136", "0", "0"], ["SKCM", "341", "385", "374", "0", "372", "0", "354", "205", "344"], ["STAD", "311", "352", "373", "0", "274", "0", "323", "264", "221"], ["THCA", "484", "494", "496", "0", "494", "0", "495", "222", "402"], ["UCEC", "482", "525", "532", "54", "527", "0", "513", "200", "248"], ["UCS", "57", "56", "57", "0", "57", "0", "56", "0", "57"], ["Totals", "7920", "8947", "8965", "2217", "7893", "1135", "7993", "4033", "5538"]], "row_count": 32, "column_count": 10, "numeric_cells": 279, "header_rows": 1, "locator": "section[1]/table-wrap[1]#pone-0106397-t001"}}, {"id": "asset:table:pmid:25181531:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:76830d0afd55d9409cd224f84e3ba7ed6af23468ae567ebb5a88b6e153500612", "bytes": 1885, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#pone-0106397-t002", "version": null, "note": "Data types supported by RTCGAToolbox.", "structure": {"pmcid": "PMC4152273", "section_index": 5, "section_title": "RTCGAToolbox Data Client and Analysis Functions", "row_count": 13, "column_count": 3}, "table": {"label": "Table 2", "caption": "Data types supported by RTCGAToolbox.", "rows": [["Data Type (Parameter)", "Description", "Output Object (FirehoseData)"], ["Clinic", "Provides clinical information for each sample. Clinical information may include stage, survival time, sex, age and more.", "fd@Clinical (data frame)"], ["RNAseq_Gene or/and RNAseq2_Gene_Norm", "Gene level expression data from RNA-seq platforms. This parameter provides raw counts and normalized values. Firehose provides 2 different algorithms for RNAseq data processing. (Data types can be specified by using RNAseqNorm and RNAseq2Norm parameters)", "fd@ RNASeqGene, fd@ RNASeq2GeneNorm (data matrix)"], ["miRNASeq_Gene", "miRNA expression levels from next generation sequencing platforms", "fd@ miRNASeqGene (data matrix)"], ["CNA_SNP", "Segmented copy number alterations (in somatic cells)", "fd@ CNASNP (data frame)"], ["CNV_SNP", "Segmented copy number variations (in germline cells)", "fd@ CNVSNP (data frame)"], ["CNA_Seq", "Copy number alterations provided by next generation sequencing platforms", "fd@ CNAseq (data frame)"], ["CNA_CGH", "Copy number alterations provided by CGH array platforms", "fd@ CNACGH (a list of FirehoseCGHArray objects)"], ["Methylation", "Methylation data provided by array platforms", "fd@ Methylation (a list of FirehoseMethylationArray object)"], ["Mutation", "Gene level mutation information matrix", "fd@ Mutations (data frame)"], ["mRNA_Array", "Gene level expression data provided by array platforms", "fd@ mRNAArray(a list of FirehosemRNAArray objects)"], ["miRNA_Array", "miRNA expression data provided by array platforms", "fd@ miRNAArray (a list of FirehosemRNAArray objects)"], ["RPPA", "Reverse phase protein array (RPPA) expression", "fd@ RPPAArray(a list of FirehosemRNAArray objects)"]], "row_count": 13, "column_count": 3, "numeric_cells": 1, "header_rows": 1, "locator": "section[5]/table-wrap[1]#pone-0106397-t002"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "It takes sample barcodes to differentiate between “Normal” and “Tumor” samples, and compares them with linear models and empirical Bayesian methods provided by the limma [20] package."}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files and http://mksamur.github.io/RTCGAToolbox."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:25181531", "asset:table:pmid:25181531:1", "asset:table:pmid:25181531:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:45Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 51280, "completion_tokens": 3068, "cached_tokens": 44688}}, "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:25181531", "type": "paper", "label": "pmid:25181531"}, {"id": "source:pmid:25181531", "type": "manuscript", "label": "PMID 25181531 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25181531", "type": "paper", "label": "pmid:25181531"}, {"id": "source:pmid:25181531", "type": "manuscript", "label": "PMID 25181531 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25181531", "type": "extraction", "used": ["source:pmid:25181531"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:25181531", "parent_hash": "sha256:a00dbf61852b163066747c6876384f13d7c4018a7328aa2c2523514b8c486203", "fork_of": null, "generation": 7}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["It takes sample barcodes to differentiate between “Normal” and “Tumor” samples, and compares them with linear models and empirical Bayesian methods provided by the limma [20] package."], "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":"2026-11-04T00:32:49+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}}}