{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39333689", "kind": "science-record", "revision": 3, "content_hash": "sha256:0fe2192cf9311b030c9a361329dcbccb9ca6ac5025c1641221c857e4dc9f86bf", "created_at": "2026-11-01T20:29:31Z", "updated_at": "2026-11-01T22:12:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction of store-operated calcium entry-related gene signature for predicting prognosis and indicates immune microenvironment infiltration in stomach adenocarcinomas.", "doi": "10.1038/s41598-024-73324-9", "pmid": "39333689", "authors": ["Zichao Zhang", "Chenglong Wang", "Wenzheng Shi", "Zhihui Wang", "Weihua Fu"], "journal": "Scientific reports", "year": 2024, "abstract": "Gastric adenocarcinoma (STAD) is the most prevalent malignancy of the human digestive system and the fourth leading cause of cancer-related death. Calcium pools, especially Ca2+ entry (SOCE) for storage operations, play a crucial role in maintaining intracellular and extracellular calcium balance, influencing cell activity, and facilitating tumor progression. Nevertheless, the prognostic and immunological value of SOCE in STAD has not been systematically studied. The objective of this study was to develop a risk model for SOCE signature and to explore its correlation with clinical characteristics, prognosis, tumor microenvironment (TME), as well as response to immunotherapy, chemotherapy, and targeted drugs. We used the TCGA, GEO (GSE84437 and GSE159929), cBioPortal and TIMER databases to acquire mRNA expression data for STAD, along with patient clinical indicators, single-cell sequencing data, genomic variation information, and correlations of immune cell infiltration. An analysis of SOCE genes based on tumor vs. normal tissue comparisons, pan-cancer dimension, single-cell sequencing, DNA mutation, and copy number variation revealed that SOCE genes significantly impact the survival of STAD patients and are differentially involved in the immune response. SOCE co-expressed genes were identified by Pearson analysis, and subsequently protein-protein interaction (PPI) and gene function enrichment analysis indicated that coexpressed genes were associated with multicellular pathways. Based on TCGA and GSE84437 datasets, a multifactor Cox proportional hazard regression analysis was conducted to identify SOCE co-expressed genes associated with overall survival in STAD patients. Several mRNA prognostic genes, including PTPRJ, GPR146, LTBP3, FBLN1, EFEMP2, ADAMTS7 and LBH, were identified, which could be used as effective prognostic predictors for STAD patients. In both training and test datasets, receiver operating characteristic (ROC) curves were utilized to evaluate and illustrate the predictive capability of this characteristic in forecasting overall survival of STAD patients. The qPCR and human protein atlas (HPA) were employed to assess mRNA expression and protein levels. Furthermore, the ESTIMATE, TIMER, CIBERSORT, QUANTISEQ, MCPCOUNTER, xCell and EPIC algorithms were utilized to perform immune score and analyze immune cell infiltration. It effectively revealed the difference in prognosis and immune cell infiltration in TME between high-risk and low-risk groups based on the risk signature associated with SOCE. Notably, significant differences in tumor immune dysfunction and rejection (TIDE) scores between the two groups, suggesting that patients in the low-risk group may exhibit a more favorable response to ICIS treatment. The GDSC database and R packages for predictive analysis were utilized to analyze responses to chemotherapy and targeted drugs in high-risk and low-risk groups. In summary, the 7-gene signature associated with SOCE serves as a significant biomarker for evaluating the TME and predicting the prognosis of STAD patients. In addition, it may provide valuable insights for developing effective immunotherapy and chemotherapy regiments for patients with STAD.", "claims": [{"id": "claim-method", "statement": "Then, multivariate COX proportional hazards regression analysis was performed using bivariate regression to screen out genes associated with prognosis in STAD patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39333689", "locator": "sections[9] \"Construction and evaluation of identified prognostic signature\" paragraph 2", "quote": "Then, multivariate COX proportional hazards regression analysis was performed using bivariate regression to screen out genes associated with prognosis in STAD patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during the current study are available in the TCGA (https://xenabrowser.net) and GEO (https://www.ncbi.nlm.nih.gov/geo/) public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open-source data, so there are no ethical issues and other conflicts of interest.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39333689", "locator": "sections[32] \"notes\" paragraph 1", "quote": "The datasets generated during the current study are available in the TCGA (https://xenabrowser.net) and GEO (https://www.ncbi.nlm.nih.gov/geo/) public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open-source data, so there are no ethical issues and other conflicts of interest."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The seven-gene SOCE-correlated risk signature stratified STAD patients into groups with significantly different overall survival, with higher risk scores associated with worse prognosis and increased mortality.", "kind": "quantitative", "target": {"value": 0.0001, "unit": "p-value", "tolerance": null, "source": "Survival analysis revealed a significantly higher survival rate in the low-risk group compared to the high-risk group (Logrank P < 0.0001, Fig. 5A)."}, "evidence": [{"asset": "source:pmid:39333689", "locator": "sections[20] \"Establishment of multigene Cox prognostic signature based on SOCE-related genes\" paragraph 3", "quote": "Survival analysis revealed a significantly higher survival rate in the low-risk group compared to the high-risk group (Logrank P < 0.0001, Fig. 5A)."}, {"asset": "source:pmid:39333689", "locator": "sections[20] \"Establishment of multigene Cox prognostic signature based on SOCE-related genes\" paragraph 3", "quote": "The findings suggest that higher the signature prognostic score is associated with worse the prognosis and increased mortality among STAD patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The seven-gene SOCE-correlated risk signature stratified STAD patients into groups with significantly different overall survival, with higher risk scores associated with worse prognosis and increased mortality.", "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:39333689"], "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:GSE159929"], "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:GSE159929"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39333689", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-73324-9", "sha256": "sha256:12c6b3539b0ab2103aa694d18299be44faf5f7903f159c86cca1620c357e4953", "bytes": 55604, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-73324-9", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11436956", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE159929", "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=GSE159929", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE159929", "version": null, "note": "The datasets generated during the current study are available in the TCGA (https://xenabrowser.net) and GEO (https://www.ncbi.nlm.nih.gov/geo/) public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open-source data, so there are no ethical issues and other conflicts of interest.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during the current study are available in the TCGA (https://xenabrowser.net) and GEO (https://www.ncbi.nlm.nih.gov/geo/) public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open-source data, so there are no ethical issues and other conflicts of interest.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4850577", "GSM4850578", "GSM4850579", "GSM4850580", "GSM4850581", "GSM4850582", "GSM4850583", "GSM4850584", "GSM4850585", "GSM4850586", "GSM4850587", "GSM4850588", "GSM4850589", "GSM4850590", "GSM4850591", "GSM4909947", "GSM4909948", "GSM4909949", "GSM4909950", "GSM4909951", "GSM4909952", "GSM4909953", "GSM4909954", "GSM4909955", "GSM4909956", "GSM4909957", "GSM4909958", "GSM4909959", "GSM4909960", "GSM4909961", "GSM4909962", "GSM4909963", "GSM4909964", "GSM4909965", "GSM4909966", "GSM4909967", "GSM4909968", "GSM4909969", "GSM4909970", "GSM4909971", "GSM4909972", "GSM4909973", "GSM4909974", "GSM4909975", "GSM4909976"], "sample_count": 45, "group_sizes": null, "group_sizes_basis": null, "platform": "20795", "taxon": "Homo sapiens", "title": "Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE84437", "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=GSE84437", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84437", "version": null, "note": "The datasets generated during the current study are available in the TCGA (https://xenabrowser.net) and GEO (https://www.ncbi.nlm.nih.gov/geo/) public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open-source data, so there are no ethical issues and other conflicts of interest.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during the current study are available in the TCGA (https://xenabrowser.net) and GEO (https://www.ncbi.nlm.nih.gov/geo/) public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. 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A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE84437", "GSE159929"], "resolved_accessions": ["GSE84437", "GSE159929"], "statements": ["The datasets generated during the current study are available in the TCGA (https://xenabrowser.net) and GEO (https://www.ncbi.nlm.nih.gov/geo/) public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open-source data, so there are no ethical issues and other conflicts of interest."], "basis": "The paper names GSE84437, GSE159929 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:39333689", "data:geo:GSE159929"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE159929"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:33:12Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14275, "completion_tokens": 2051, "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:39333689", "type": "paper", "label": "pmid:39333689"}, {"id": "source:pmid:39333689", "type": "manuscript", "label": "PMID 39333689 full text"}, {"id": "data:geo:GSE159929", "type": "dataset", "label": "GEO GSE159929"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39333689", "type": "paper", "label": "pmid:39333689"}, {"id": "source:pmid:39333689", "type": "manuscript", "label": "PMID 39333689 full text"}, {"id": "data:geo:GSE159929", "type": "dataset", "label": "GEO GSE159929"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39333689", "type": "extraction", "used": ["source:pmid:39333689"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE159929", "type": "accession_resolution", "used": ["data:geo:GSE159929"], "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:39333689", "parent_hash": "sha256:298e076a6c64acf4e48a924cba3852b1b3b4332daa3b29803cbe9d0ddba6a2bd", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE159929 licence not read", "asset:data:geo:GSE159929 not downloaded", "asset:data:geo:GSE84437 licence not read", "asset:data:geo:GSE84437 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["sting overall survival of STAD patients. The qPCR and human protein atlas (HPA) were employed", "time quantitative polymerase chain reaction (RT-qPCR, Table S1) using SYBR Premix Ex Taq II kit (", "e quantitative polymerase chain reaction (RT-qPCR, Table S1) using SYBR Premix Ex Taq II kit ("], "order_basis": "paper_text_order:2239", "id": "assay:1"}, {"role": "data_generation", "definition_id": "methylation_array", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["CIBERSORT, QUANTISEQ, MCPCOUNTER, xCell and EPIC algorithms were utilized to perform immune s"], "order_basis": "paper_text_order:2413", "id": "assay:2"}, {"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": ["Sciences in Shanghai, China. The cells were cultured in RPMI 1640 (BasaMedia, Shanghai, China) suppl"], "order_basis": "paper_text_order:3624", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ated. The HPA online tool was used to obtain immunohistochemistry-based protein expression profiles in normal"], "order_basis": "paper_text_order:4441", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Then, multivariate COX proportional hazards regression analysis was performed using bivariate regression to screen out genes associated with prognosis in STAD patients."], "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":"2026-11-04T01:25:36+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}}}