{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33990536", "kind": "science-record", "revision": 9, "content_hash": "sha256:29feefe9d339fb02f00ad70610fb476105e0e19f380cebdb43b2919cbd773294", "created_at": "2026-11-01T15:41:35Z", "updated_at": "2026-11-01T22:46:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "H Long Terminal Repeat-Associating 2 (HHLA2) is a Biomarker of Advanced Stage Hepatocellular Carcinoma and Promotes Tumor Cell Development In Vitro.", "doi": "10.12659/MSM.930215", "pmid": "33990536", "authors": ["Min Luo", "Yao Xiong", "Yan Lin", "Rong Liang", "Yongqiang Li", "Lianying Ge"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2021, "abstract": "BACKGROUND Several risk factors contribute to the inflammation promoting hepatocellular carcinoma (HCC) development, but the underlying mechanisms are unknown. Human endogenous retrovirus H long terminal repeat-associating 2 (HHLA2), a B7 family member, is highly expressed in various malignant tumor tissues and is related to tumor progression and metastasis. MATERIAL AND METHODS Bioinformatics analysis was used to analyze the gene expression chip GSE33006 of HCC tissue in the GEO database, draw a heat map of differentially expressed genes, and analyze the GO pathway of gene function annotation. Then, we compared HCC tissues with para-carcinoma liver tissues from 55 patients for expression patterns and associations with HHLA2. Effects of HHLA2 knockdown were examined in the human HCC cell line HepG2 to explore effects of HHLA2 on HepG2 cells. RESULTS A significantly higher expression of HHLA2 at the mRNA and protein levels was detected in HCC tissues than in para-carcinoma liver tissues, which was similar to HHLA2 expression in the GSE33006 data. A higher expression of HHLA2 protein was associated with advanced cancer stage, tumor differentiation, and invasion of adjacent structures. In vitro knockdown of HHLA2 expression significantly increased HepG2 cell adhesion, promoted cell apoptosis, induced cell cycle arrest in the G1/S phase, and inhibited cell proliferation, migration, and invasion. CONCLUSIONS Our data indicated there was a higher expression of HHLA2 in HCC tissues than in para-carcinoma liver tissues, and HHLA2 plays a major role in the development and progression of HCC. Owing to its higher expression, HHLA2 is a potential prognostic biomarker for HCC.", "claims": [{"id": "claim-method", "statement": "Differences between groups were assessed using the t test or Mann-Whitney U test, based on data distribution. One-way analysis of variance (ANOVA) was used when more than 2 groups were compared.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33990536", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "Differences between groups were assessed using the t test or Mann-Whitney U test, based on data distribution. One-way analysis of variance (ANOVA) was used when more than 2 groups were compared."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data on 3 HCC samples and 3 para-carcinoma samples were retrieved from the human HCC transcriptional chip GSE33006 in the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo) [10].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33990536", "locator": "sections[3] \"Data Source\" paragraph 2", "quote": "Data on 3 HCC samples and 3 para-carcinoma samples were retrieved from the human HCC transcriptional chip GSE33006 in the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo) [10]."}], "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:33990536"], "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:GSE33006"], "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:GSE33006"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33990536", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.930215", "sha256": "sha256:24196556ca454d313459ac6c7ae0daae5e3492f728c45c38016e421bd38e6ca9", "bytes": 27117, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.930215", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8132585", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE33006", "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=GSE33006", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33006", "version": null, "note": "Data on 3 HCC samples and 3 para-carcinoma samples were retrieved from the human HCC transcriptional chip GSE33006 in the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo) [10].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data on 3 HCC samples and 3 para-carcinoma samples were retrieved from the human HCC transcriptional chip GSE33006 in the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo) [10].", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM818276", "GSM818277", "GSM818278", "GSM818279", "GSM818280", "GSM818281"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiles from the hepatocellular carcinoma (HCC) tissues", "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:33990536:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4ea5c6d6df98ac4cedc5ba07992a2c5b6b8dbaae1df6515bab7c2c108a1d78f0", "bytes": 1533, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#t1-medscimonit-27-e930215", "version": null, "note": "Summary of the clinicopathological characteristics of patients with hepatocellular carcinoma and HHLA2 protein expression.", "structure": {"pmcid": "PMC8132585", "section_index": 4, "section_title": "Patients and Samples", "row_count": 31, "column_count": 5}, "table": {"label": "Table 1", "caption": "Summary of the clinicopathological characteristics of patients with hepatocellular carcinoma and HHLA2 protein expression.", "rows": [["Characteristic", "Number of patients", "HHLA2 expression", "P vaule"], ["χ̄±s"], ["Gender", "Male", "48", "0.910±0.280", "0.058"], ["Female", "7", "0.700±0.133"], ["Age (years)", "≤55", "23", "0.940±0.229", "0.216"], [">55", "32", "0.846±0.299"], ["Smoking", "No", "35", "0.857±0.278", "0.348"], ["Yes", "20", "0.930±0.269"], ["Drinking", "No", "42", "0.860±0.276", "0.261"], ["Yes", "13", "0.956±0.268"], ["BCLC stage", "A", "33", "0.726±0.206", "<0.001**"], ["B", "7", "1.006±0.233"], ["C", "15", "1.137±0.126"], ["Differentiation", "High and moderate", "34", "0.811±0.272", "0.008**"], ["Poor", "21", "1.008±0.237"], ["AFP (ng/ml)", "≤200", "32", "0.855±0.246", "0.237"], [">200", "23", "0.940±0.278"], ["Tumour capsular", "No", "45", "0.889±0.288", "0.733"], ["Yes", "10", "0.856±0.215"], ["Tumor size (cm)", "≤5", "21", "0.839±0.280", "0.355"], [">5", "34", "0.910±0.272"], ["HBV infection", "No", "16", "0.842±0.217", "0.481"], ["Yes", "39", "0.900±0.296"], ["Liver cirrhosis", "No", "32", "0.828±0.308", "0.078"], ["Yes", "23", "0.960±0.201"], ["Adjacent structures invasion", "No", "45", "0.837±0.274", "0.007**"], ["Yes", "10", "1.090±0.166"], ["PVTT", "No", "47", "0.855±0.277", "0.060"], ["Yes", "8", "1.051±0.197"], ["Lymph node metastasis", "No", "49", "0.875±0.286", "0.520"], ["Yes", "6", "0.952±0.146"]], "row_count": 31, "column_count": 5, "numeric_cells": 78, "header_rows": 2, "locator": "section[4]/table-wrap[1]#t1-medscimonit-27-e930215"}}, {"id": "asset:table:pmid:33990536:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:027ee1467b8253fc963e83c80bd8a24a30742228cc308fddccaa385c4dac0ff4", "bytes": 382, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#t2-medscimonit-27-e930215", "version": null, "note": "The expression level of HHLA2 mRNA in HepG2 cells.", "structure": {"pmcid": "PMC8132585", "section_index": 17, "section_title": "In Vitro Knockdown of HHLA2 in the HCC Cell Line HepG2", "row_count": 5, "column_count": 2}, "table": {"label": "Table 2", "caption": "The expression level of HHLA2 mRNA in HepG2 cells.", "rows": [["Group", "HHLA2 mRNA expression"], ["HepG2-NC", "1.003±0.092"], ["HepG2+shRNA 1", "0.300±0.013*"], ["HepG2+shRNA 2", "0.997±0.071"], ["HepG2+shRNA 3", "0.992±0.028"]], "row_count": 5, "column_count": 2, "numeric_cells": 7, "header_rows": 1, "locator": "section[17]/table-wrap[1]#t2-medscimonit-27-e930215"}}], "gaps": ["asset:data:geo:GSE33006 not downloaded", "asset:data:geo:GSE33006 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": "Differences between groups were assessed using the t test or Mann-Whitney U test, based on data distribution. One-way analysis of variance (ANOVA) was used when more than 2 groups were compared."}}, {"id": "method-2", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann-Whitney"}}], "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": ["GSE33006"], "resolved_accessions": ["GSE33006"], "statements": ["Data on 3 HCC samples and 3 para-carcinoma samples were retrieved from the human HCC transcriptional chip GSE33006 in the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo) [10]."], "basis": "The paper names GSE33006 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:33990536", "data:geo:GSE33006", "asset:table:pmid:33990536:1", "asset:table:pmid:33990536:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE33006"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:29:56Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 22786, "completion_tokens": 886, "cached_tokens": 792}}, "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:33990536", "type": "paper", "label": "pmid:33990536"}, {"id": "source:pmid:33990536", "type": "manuscript", "label": "PMID 33990536 full text"}, {"id": "data:geo:GSE33006", "type": "dataset", "label": "GEO GSE33006"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33990536", "type": "paper", "label": "pmid:33990536"}, {"id": "source:pmid:33990536", "type": "manuscript", "label": "PMID 33990536 full text"}, {"id": "data:geo:GSE33006", "type": "dataset", "label": "GEO GSE33006"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33990536", "type": "extraction", "used": ["source:pmid:33990536"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE33006", "type": "accession_resolution", "used": ["data:geo:GSE33006"], "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:33990536", "parent_hash": "sha256:de9695d279a218d540964bd68c552f6ec2ee19b81fec90f0d77adb804b7078b7", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE33006 licence not read", "asset:data:geo:GSE33006 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": 0.99, "evidence": ["nd associations with HHLA2. Effects of HHLA2 knockdown were examined in the human HCC cell line Hep", "nd invasion of adjacent structures. In vitro knockdown of HHLA2 expression significantly increased"], "order_basis": "paper_text_order:857", "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": 0.99, "evidence": ["own were examined in the human HCC cell line HepG2 to explore effects of HHLA2 on HepG2 cells.", "ll line HepG2 to explore effects of HHLA2 on HepG2 cells. RESULTS A significantly higher expres", "of HHLA2 expression significantly increased HepG2 cell adhesion, promoted cell apoptosis, indu"], "order_basis": "paper_text_order:908", "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": 0.69, "evidence": ["increased HepG2 cell adhesion, promoted cell apoptosis, induced cell cycle arrest in the G1/S phase"], "order_basis": "paper_text_order:1404", "id": "assay:3"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["es and para-carcinoma tissues by qRT-PCR and western blot analysis. Eleven normal liver tissues were u", "(both *** P<0.001). (B) Respective cases by western blot showing HHLA2 protein levels in paired sampl"], "order_basis": "paper_text_order:3819", "id": "assay:4"}, {"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": ["Differences between groups were assessed using the t test or Mann-Whitney U test, based on data distribution. One-way analysis of variance (ANOVA) was used when more than 2 groups were compared."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]},"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":"2026-11-04T02:51:15+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}