{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37193981", "kind": "science-record", "revision": 3, "content_hash": "sha256:b0f4719c787d71f60eb4a975d30bc1d4558b4216d35acdb4be66f92ba8d7ceab", "created_at": "2026-11-01T19:01:53Z", "updated_at": "2026-11-01T22:09:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "ACSL4 serves as a novel prognostic biomarker correlated with immune infiltration in Cholangiocarcinoma.", "doi": "10.1186/s12885-023-10903-5", "pmid": "37193981", "authors": ["Shuochen Liu", "Shilong Fan", "Yirui Wang", "Ruixiang Chen", "Ziyi Wang", "Yaodong Zhang", "Wangjie Jiang", "Yananlan Chen", "Xiao Xu", "Yue Yu", "Changxian Li", "Xiangcheng Li"], "journal": "BMC cancer", "year": 2023, "abstract": "BACKGROUND: Cholangiocarcinoma (CHOL) is the second most common primary hepatic malignant tumor, following hepatocellular carcinoma (HCC). CHOL is highly aggressive and heterogeneous resulting in poor prognosis. The diagnosis and prognosis of CHOL has not improved in the past decade. Acyl-CoA synthetase long-chain family member 4 (ACSL4) is reported to be associated with tumors, however, its role in CHOL has not been revealed. This study is mainly for exploring the prognostic values and potential function of ACSL4 in CHOL.\nMETHODS: We investigated the expression level and prognostic value of ACSL4 in CHOL based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. TIMER2.0, TISIDB and CIBERSORT databases were utilized to assess the associations between ACSL4 and immune infiltration cells in CHOL. Single-cell sequencing data from GSE138709 was analyzed to study the expression of ACSL4 in different types of cells. ACSL4 co-expressed genes were analyzed by Linkedomics. Additionally, Western Blot, qPCR, EdU assay, CCK8 assay, transwell assay and wound healing assay were performed to further confirm the roles of ACSL4 in the pathogenesis of CHOL.\nRESULTS: We found that the level of ACSL4 was higher in CHOL and it was correlated with the diagnosis and prognosis of CHOL patients. Then, we observed that the infiltration level of immune cells was related to the level of ACSL4 in CHOL. Moreover, ACSL4 and its co-expressed genes were mainly enriched in metabolism-related pathway and ACSL4 is also a key pro-ferroptosis gene in CHOL. Finally, knockdown of ACSL4 could reverse the tumor-promoting effect of ACSL4 in CHOL.\nCONCLUSIONS: The current findings demonstrated ACSL4 may as a novel biomarker for CHOL patients, which might regulate immune microenvironment and metabolism resulting in poor prognosis.", "claims": [{"id": "claim-method", "statement": "Associations were evaluated using Spearman’s correlation analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37193981", "locator": "sections[14] \"Statistical analysis\" paragraph 2", "quote": "Associations were evaluated using Spearman’s correlation analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented during this study are included in this published article. The datasets analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo, GEO accession number: GSE76297, GSE107943 and GSE138709), TCGA repository (https://www.cancer.gov/tcga), TIMER2.0 repository (http://timer.cistrome.org/), HPA repository (http://www.proteinatlas.org/), TISIDB repository (http://cis.hku.hk/TISIDB/), LinkedOmics repository (http://www.linkedomics.org/login.php).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37193981", "locator": "sections[30] \"notes\" paragraph 1", "quote": "The original contributions presented during this study are included in this published article. The datasets analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo, GEO accession number: GSE76297, GSE107943 and GSE138709), TCGA repository (https://www.cancer.gov/tcga), TIMER2.0 repository (http://timer.cistrome.org/), HPA repository (http://www.proteinatlas.org/), TISIDB repository (http://cis.hku.hk/TISIDB/), LinkedOmics repository (http://www.linkedomics.org/login.php)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:37193981"], "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:GSE107943"], "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:GSE107943"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37193981", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-023-10903-5", "sha256": "sha256:8aef8a23ff4b4b58cbb2d4a9f26ac4c2b14f45d8e1845fa7bbb81d85cdff4783", "bytes": 34673, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-023-10903-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10186676", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE107943", "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=GSE107943", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE107943", "version": null, "note": "The original contributions presented during this study are included in this published article. The datasets analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo, GEO accession number: GSE76297, GSE107943 and GSE138709), TCGA repository (https://www.cancer.gov/tcga), TIMER2.0 repository (http://timer.cistrome.org/), HPA repository (http://www.proteinatlas.org/), TISIDB repository (http://cis.hku.hk/TISIDB/), LinkedOmics repository (http://www.linkedomics.org/login.php).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented during this study are included in this published article. The datasets analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo, GEO accession number: GSE76297, GSE107943 and GSE138709), TCGA repository (https://www.cancer.gov/tcga), TIMER2.0 repository (http://timer.cistrome.org/), HPA repository (http://www.proteinatlas.org/), TISIDB repository (http://cis.hku.hk/TISIDB/), LinkedOmics repository (http://www.linkedomics.org/login.php).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2883928", "GSM2883929", "GSM2883930", "GSM2883931", "GSM2883932", "GSM2883933", "GSM2883934", "GSM2883935", "GSM2883936", "GSM2883937", "GSM2883938", "GSM2883939", "GSM2883940", "GSM2883941", "GSM2883942", "GSM2883943", "GSM2883944", "GSM2883945", "GSM2883946", "GSM2883947", "GSM2883948", "GSM2883949", "GSM2883950", "GSM2883951", "GSM2883952", "GSM2883953", "GSM2883954", "GSM2883955", "GSM2883956", "GSM2883957", "GSM2883958", "GSM2883959", "GSM2883960", "GSM2883961", "GSM2883962", "GSM2883963", "GSM2883964", "GSM2883965", "GSM2883966", "GSM2883967", "GSM2883968", "GSM2883969", "GSM2883970", "GSM2883971", "GSM2883972", "GSM2883973", "GSM2883974", "GSM2883975", "GSM2883976", "GSM2883977", "GSM2883978", "GSM2883979", "GSM2883980", "GSM2883981", "GSM2883982", "GSM2883983", "GSM2883984"], "sample_count": 57, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Integrative molecular and clinical analysis of intrahepatic cholangiocarcinoma reveals two prognostic subclassees", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE138709", "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=GSE138709", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE138709", "version": null, "note": "The original contributions presented during this study are included in this published article. 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The datasets analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo, GEO accession number: GSE76297, GSE107943 and GSE138709), TCGA repository (https://www.cancer.gov/tcga), TIMER2.0 repository (http://timer.cistrome.org/), HPA repository (http://www.proteinatlas.org/), TISIDB repository (http://cis.hku.hk/TISIDB/), LinkedOmics repository (http://www.linkedomics.org/login.php).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4116579", "GSM4116580", "GSM4116581", "GSM4116582", "GSM4116583", "GSM4116584", "GSM4116585", "GSM4116586"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "24676;20795", "taxon": "Homo sapiens", "title": "Dissecting the transcriptomic landscape of the human intrahepatic cholangiocarcinoma by single cell RNA-sequencing", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE76297", "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=GSE76297", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76297", "version": null, "note": "The original contributions presented during this study are included in this published article. 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"blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE76297", "GSE107943", "GSE138709"], "resolved_accessions": ["GSE76297", "GSE107943", "GSE138709"], "statements": ["The original contributions presented during this study are included in this published article. The datasets analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo, GEO accession number: GSE76297, GSE107943 and GSE138709), TCGA repository (https://www.cancer.gov/tcga), TIMER2.0 repository (http://timer.cistrome.org/), HPA repository (http://www.proteinatlas.org/), TISIDB repository (http://cis.hku.hk/TISIDB/), LinkedOmics repository (http://www.linkedomics.org/login.php)."], "basis": "The paper names GSE76297, GSE107943, GSE138709 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": ["survival_km"], "assets": ["source:pmid:37193981", "data:geo:GSE107943"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE107943"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:40:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10865, "completion_tokens": 3230, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37193981", "type": "paper", "label": "pmid:37193981"}, {"id": "source:pmid:37193981", "type": "manuscript", "label": "PMID 37193981 full text"}, {"id": "data:geo:GSE107943", "type": "dataset", "label": "GEO GSE107943"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37193981", "type": "paper", "label": "pmid:37193981"}, {"id": "source:pmid:37193981", "type": "manuscript", "label": "PMID 37193981 full text"}, {"id": "data:geo:GSE107943", "type": "dataset", "label": "GEO GSE107943"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37193981", "type": "extraction", "used": ["source:pmid:37193981"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE107943", "type": "accession_resolution", "used": ["data:geo:GSE107943"], "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:37193981", "parent_hash": "sha256:92a5bc3ef5b5cb9930276bc72e4c756c290dd93d7486664fa5f266a1c53d268e", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE107943 licence not read", "asset:data:geo:GSE107943 not downloaded", "asset:data:geo:GSE138709 licence not read", "asset:data:geo:GSE138709 not downloaded", "asset:data:geo:GSE76297 licence not read", "asset:data:geo:GSE76297 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["were analyzed by Linkedomics. Additionally, Western Blot, qPCR, EdU assay, CCK8 assay, transwell assa"], "order_basis": "paper_text_order:1079", "id": "assay:1"}, {"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": ["by Linkedomics. Additionally, Western Blot, qPCR, EdU assay, CCK8 assay, transwell assay and"], "order_basis": "paper_text_order:1093", "id": "assay:2"}, {"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": ["Additionally, Western Blot, qPCR, EdU assay, CCK8 assay, transwell assay and wound healing ass"], "order_basis": "paper_text_order:1109", "id": "assay:3"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["a key pro-ferroptosis gene in CHOL. Finally, knockdown of ACSL4 could reverse the tumor-promoting e", "ng to regional regulations. Cell culture and transfection Human intrahepatic biliary epithelial cell l", "0 (11,668,019, Invitrogen, USA) was used for transfection following the manufacturer’s protocol. The f", "g the manufacturer’s protocol. The following siRNA sequences were used: ACSL4 sense 5′-GAGGCUUC"], "order_basis": "paper_text_order:1639", "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": 0.77, "evidence": ["9 were used in our study. All the cells were cultured in DMEM High Glucose (Biochannel, China) contai"], "order_basis": "paper_text_order:2535", "id": "assay:5"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Kaplan-Meier"], "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":"2026-11-04T02:52:35+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}}}