{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35722095", "kind": "science-record", "revision": 4, "content_hash": "sha256:ed4d7e658b5e011a53529d978c1890645d0156d63bed5bbe3782f8cc9c86ad16", "created_at": "2026-11-01T18:14:44Z", "updated_at": "2026-11-01T22:06:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Human Plasma Transcriptome Implicates Dysregulated S100A12 Expression: A Strong, Early-Stage Prognostic Factor in ST-Segment Elevated Myocardial Infarction: Bioinformatics Analysis and Experimental Verification.", "doi": "10.3389/fcvm.2022.874436", "pmid": "35722095", "authors": ["Hu Zhai", "Lei Huang", "Yijie Gong", "Yingwu Liu", "Yu Wang", "Bojiang Liu", "Xiandong Li", "Chunyan Peng", "Tong Li"], "journal": "Frontiers in cardiovascular medicine", "year": 2022, "abstract": "The ability of blood transcriptome analysis to identify dysregulated pathways and outcome-related genes following myocardial infarction remains unknown. Two gene expression datasets (GSE60993 and GSE61144) were downloaded from Gene Expression Omnibus (GEO) Datasets to identify altered plasma transcriptomes in patients with ST-segment elevated myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention. GEO2R, Gene Ontology/Kyoto Encyclopedia of Genes and Genomes annotations, protein-protein interaction analysis, etc., were adopted to determine functional roles and regulatory networks of differentially expressed genes (DEGs). Dysregulated expressomes were verified at transcriptional and translational levels by analyzing the GSE49925 dataset and our own samples, respectively. A total of 91 DEGs were identified in the discovery phase, consisting of 15 downregulated genes and 76 upregulated genes. Two hub modules consisting of 12 hub genes were identified. In the verification phase, six of the 12 hub genes exhibited the same variation patterns at the transcriptional level in the GSE49925 dataset. Among them, S100A12 was shown to have the best discriminative performance for predicting in-hospital mortality and to be the only independent predictor of death during follow-up. Validation of 223 samples from our center showed that S100A12 protein level in plasma was significantly lower among patients who survived to discharge, but it was not an independent predictor of survival to discharge or recurrent major adverse cardiovascular events after discharge. In conclusion, the dysregulated expression of plasma S100A12 at the transcriptional level is a robust early prognostic factor in patients with STEMI, while the discrimination power of the protein level in plasma needs to be further verified by large-scale, prospective, international, multicenter studies.", "claims": [{"id": "claim-method", "statement": "Using median values as the cutoff values for the markers, receiver operating characteristic curve analysis was used to measure their discriminative performances for promising early biomarkers of mortality. Both univariate (unadjusted) and multivariate (adjusted) logistic regression were performed to determine independent clinical factors and biomarkers that were associated with death. A multivariate regression analysis was performed via a Cox proportional hazard regression model, aiming to identify factors that might independently influence survival.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35722095", "locator": "sections[10] \"Statistical Analyses\" paragraph 2", "quote": "Using median values as the cutoff values for the markers, receiver operating characteristic curve analysis was used to measure their discriminative performances for promising early biomarkers of mortality."}, {"asset": "source:pmid:35722095", "locator": "sections[10] \"Statistical Analyses\" paragraph 2", "quote": "Both univariate (unadjusted) and multivariate (adjusted) logistic regression were performed to determine independent clinical factors and biomarkers that were associated with death."}, {"asset": "source:pmid:35722095", "locator": "sections[10] \"Statistical Analyses\" paragraph 2", "quote": "A multivariate regression analysis was performed via a Cox proportional hazard regression model, aiming to identify factors that might independently influence survival."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in the GEO Datasets [GSE61144 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61144), GSE60993 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60993), and GSE49925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49925)]. As open access to individual-level data was not specified in the original application approved by the ethics committee, the underlying data are only available upon reasonable request. Please contact the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35722095", "locator": "sections[22] \"Data Availability Statement\" paragraph 2", "quote": "The datasets generated and/or analyzed during the current study are available in the GEO Datasets [GSE61144 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61144), GSE60993 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60993), and GSE49925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49925)]. As open access to individual-level data was not specified in the original application approved by the ethics committee, the underlying data are only available upon reasonable request. Please contact the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "S100A12 showed the best discriminative performance, with an area under the curve of 0.768 (95% CI, 0.588–0.949; P = 0.032), and the sensitivity and specificity were 83.3 and 69.1%, respectively.", "kind": "quantitative", "target": {"value": 0.032, "unit": "p-value", "tolerance": null, "source": "Overall, based on the median values as the cutoff value for the markers, we found that S100A12 showed the best discriminative performance, with an area under the curve of 0.768 (95% CI, 0.588–0.949; P = 0.032), and the sensitivity and specificity were 83.3 and 69.1%, respectively (Supplementary Table 7)."}, "evidence": [{"asset": "source:pmid:35722095", "locator": "sections[18] \"Discriminative Performance of the Early Biomarkers to Mortality\" paragraph 2", "quote": "Overall, based on the median values as the cutoff value for the markers, we found that S100A12 showed the best discriminative performance, with an area under the curve of 0.768 (95% CI, 0.588–0.949; P = 0.032), and the sensitivity and specificity were 83.3 and 69.1%, respectively (Supplementary Table 7)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "S100A12 showed the best discriminative performance, with an area under the curve of 0.768 (95% CI, 0.588–0.949; P = 0.032), and the sensitivity and specificity were 83.3 and 69.1%, respectively.", "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:35722095"], "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:GSE49925"], "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:GSE49925"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35722095", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcvm.2022.874436", "sha256": "sha256:9b736b84e0932faf6b677dd4be7993992e9b7855db04265a4b37543005df872d", "bytes": 56036, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcvm.2022.874436", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9200219", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE49925", "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=GSE49925", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE49925", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in the GEO Datasets [GSE61144 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61144), GSE60993 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60993), and GSE49925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49925)]. 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"title": "Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE60993", "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=GSE60993", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE60993", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in the GEO Datasets [GSE61144 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61144), GSE60993 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60993), and GSE49925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49925)]. As open access to individual-level data was not specified in the original application approved by the ethics committee, the underlying data are only available upon reasonable request. Please contact the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in the GEO Datasets [GSE61144 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61144), GSE60993 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60993), and GSE49925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49925)]. As open access to individual-level data was not specified in the original application approved by the ethics committee, the underlying data are only available upon reasonable request. Please contact the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1495313", "GSM1495314", "GSM1495315", "GSM1495316", "GSM1495317", "GSM1495318", "GSM1495319", "GSM1495320", "GSM1495321", "GSM1495322", "GSM1495323", "GSM1495324", "GSM1495325", "GSM1495326", "GSM1495327", "GSM1495328", "GSM1495329", "GSM1495330", "GSM1495331", "GSM1495332", "GSM1495333", "GSM1495334", "GSM1495335", "GSM1495336", "GSM1495337", "GSM1495338", "GSM1495339", "GSM1495340", "GSM1495341", "GSM1495342", "GSM1495343", "GSM1495344", "GSM1495345"], "sample_count": 33, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Assessment and Diagnostic Relevance of Novel Serum Biomarkers for Early Decision of ST-elevation Myocardial Infarction", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE61144", "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=GSE61144", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE61144", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in the GEO Datasets [GSE61144 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61144), GSE60993 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60993), and GSE49925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49925)]. As open access to individual-level data was not specified in the original application approved by the ethics committee, the underlying data are only available upon reasonable request. Please contact the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in the GEO Datasets [GSE61144 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61144), GSE60993 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60993), and GSE49925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49925)]. As open access to individual-level data was not specified in the original application approved by the ethics committee, the underlying data are only available upon reasonable request. Please contact the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1498369", "GSM1498370", "GSM1498371", "GSM1498372", "GSM1498373", "GSM1498374", "GSM1498375", "GSM1498376", "GSM1498377", "GSM1498378", "GSM1498379", "GSM1498380", "GSM1498381", "GSM1498382", "GSM1498383", "GSM1498384", "GSM1498385", "GSM1498386", "GSM1498387", "GSM1498388", "GSM1498389", "GSM1498390", "GSM1498391", "GSM1498392"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "6106", "taxon": "Homo sapiens", "title": "Expression data from blood samples of STEMI and Same STEMI patients after PIC", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE49925 not downloaded", "asset:data:geo:GSE49925 licence not read", "asset:data:geo:GSE60993 not downloaded", "asset:data:geo:GSE60993 licence not read", "asset:data:geo:GSE61144 not downloaded", "asset:data:geo:GSE61144 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 1.0, "band": "reordered", "quote": "Using median values as the cutoff values for the markers, receiver operating characteristic curve analysis was used to measure their discriminative performances for promising early biomarkers of mortality. Both univariate (unadjusted) and multivariate (adjusted) logistic regression were performed to determine independent clinical factors and biomarkers that were associated with death. A multivariate regression analysis was performed via a Cox proportional hazard regression model, aiming to identify factors that might independently influence survival."}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "low-up, with a value of HR of 4"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.032, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. 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": ["glm_logit_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: logistic."}, "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": ["GSE60993", "GSE61144", "GSE49925"], "resolved_accessions": ["GSE60993", "GSE61144", "GSE49925"], "statements": ["The datasets generated and/or analyzed during the current study are available in the GEO Datasets [GSE61144 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61144), GSE60993 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60993), and GSE49925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49925)]. As open access to individual-level data was not specified in the original application approved by the ethics committee, the underlying data are only available upon reasonable request. Please contact the corresponding authors."], "basis": "The paper names GSE60993, GSE61144, GSE49925 in GEO Datasets and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["glm_logit_fit"], "assets": ["source:pmid:35722095", "data:geo:GSE49925"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE49925"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:51:31Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14954, "completion_tokens": 1931, "cached_tokens": 128}}, "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:35722095", "type": "paper", "label": "pmid:35722095"}, {"id": "source:pmid:35722095", "type": "manuscript", "label": "PMID 35722095 full text"}, {"id": "data:geo:GSE49925", "type": "dataset", "label": "GEO GSE49925"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35722095", "type": "paper", "label": "pmid:35722095"}, {"id": "source:pmid:35722095", "type": "manuscript", "label": "PMID 35722095 full text"}, {"id": "data:geo:GSE49925", "type": "dataset", "label": "GEO GSE49925"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35722095", "type": "extraction", "used": ["source:pmid:35722095"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE49925", "type": "accession_resolution", "used": ["data:geo:GSE49925"], "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:35722095", "parent_hash": "sha256:e9758ac1b06396b84feb668a4de7412a295aa9c232d3a6b5c9a533134c6037dc", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE49925 licence not read", "asset:data:geo:GSE49925 not downloaded", "asset:data:geo:GSE60993 licence not read", "asset:data:geo:GSE60993 not downloaded", "asset:data:geo:GSE61144 licence not read", "asset:data:geo:GSE61144 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": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ially Expressed Genes Identification The raw microarray data of the two datasets downloaded from the"], "order_basis": "paper_text_order:2165", "id": "assay:1"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tected by enzyme-linked immunosorbent assay (ELISA). The last follow-up date for all these part", "their S100A12 plasma levels were detected by enzyme-linked immunosorbent assay (ELISA). The last follow-up date for all the"], "order_basis": "paper_text_order:4360", "id": "assay:2"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["glm_logit_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Using median values as the cutoff values for the markers, receiver operating characteristic curve analysis was used to measure their discriminative performances for promising early biomarkers of mortality. Both univariate (unadjusted) and multivariate (adjusted) logistic regression were performed to determine independent clinical factors and biomarkers that were associated with death. A multivariate regression analysis was performed via a Cox proportional hazard regression model, aiming to identify factors that might independently influence survival."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"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":"2026-11-04T03:14:08+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}}}