{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36238495", "kind": "science-record", "revision": 5, "content_hash": "sha256:5a10bc3ab0f1f80aa2617a80bc8dfba58460a60dc37bab18812c34a0a40ac826", "created_at": "2026-11-01T18:15:37Z", "updated_at": "2026-11-01T22:50:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics and Experimental Analysis Identified TRIM28 a Potential Prognostic Biomarker and Correlated with Immune Infiltrates in Liver Hepatocellular Carcinoma.", "doi": "10.1155/2022/6267851", "pmid": "36238495", "authors": ["Jiyu Han", "Yanhong Wang", "Haichao Zhou", "Songtao Ai", "Daqian Wan"], "journal": "Computational and mathematical methods in medicine", "year": 2022, "abstract": "Background: Since the 1970s, liver hepatocellular carcinoma (LIHC) has experienced a constant rise in incidence and mortality rates, making the identification of LIHC biomarkers very important. Tripartite Motif-Containing 28 (TRIM28) is a protein-coding gene which encodes the tripartite motif-containing proteins (TRIMs) family and is associated with specific chromatin regions. TRIM28 expression and its prognostic value and impact on the immune system in LIHC patients are being investigated for the first time.\nMethods: The TRIM28 expression data from TCGA database was used to analyze TRIM28 expression, clinicopathological information, gene enrichment, and immune infiltration and conduct additional bioinformatics analysis. R language was used for statistical analysis. TIMER, CIBERSORT, and ssGSEA were used to assess immune responses of TRIM28 in LIHC. Next, the results were validated using GEPIA, ROC analysis, and immunohistochemical staining pictures from the THPA. GSE14520, GSE63898, and GSE87630 datasets were analyzed using ROC analysis to further evaluate TRIM28's diagnostic value. To ultimately determine TRIM28 expression, we performed qRT-PCR (quantitative real-time polymerase chain reaction).\nResults: High TRIM28 expression level was associated with T classification, pathologic stage, histologic grade, and serum AFP levels. In patients with LIHC, TRIM28 was an independent risk factor for a poor prognosis. The pathways ligand-receptor interaction, which is critical in LIHC patients, were closely associated with TRIM28 expression, and the function of DC could be suppressed by overexpression of TRIM28. As a final step, our results were validated by GEO data and qRT-PCR.\nConclusions: TRIM28 will shed new light on LIHC mechanisms. As an effective diagnostic and intervention tool, this gene will be able to diagnose and treat LIHC at an early stage.", "claims": [{"id": "claim-method", "statement": "To summarize, survival analysis was performed by graphing K-M survival curves with the R packages survival and survminer. The K-M survival curve was used to compare the OS and progression-free interval (PFI) between the high and low TRIM28 groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36238495", "locator": "sections[5] \"2.3. Survival Analysis Based on TRIM28 Expression\" paragraph 2", "quote": "To summarize, survival analysis was performed by graphing K-M survival curves with the R packages survival and survminer. The K-M survival curve was used to compare the OS and progression-free interval (PFI) between the high and low TRIM28 groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to 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. The qRT-PCR data used to support the findings of this study have not been made available. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63898; and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87630).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36238495", "locator": "sections[26] \"Data Availability\" paragraph 2", "quote": "The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to 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. The qRT-PCR data used to support the findings of this study have not been made available. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63898; and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87630)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "High TRIM28 expression was an independent predictor of poor prognosis in LIHC (P value <0.001), with an AUC of 0.687 for survival prediction.", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "Based on the multivariate analysis shown in Figure 2(a), TRIM28 expression (P value <0.001) has been found to be an independent predictor of poor prognosis for oncologist-patients (Table 1)."}, "evidence": [{"asset": "source:pmid:36238495", "locator": "sections[15] \"3.1. Survival Outcomes and Variable Analyses\" paragraph 3", "quote": "Based on the multivariate analysis shown in Figure 2(a), TRIM28 expression (P value <0.001) has been found to be an independent predictor of poor prognosis for oncologist-patients (Table 1)."}, {"asset": "source:pmid:36238495", "locator": "sections[15] \"3.1. Survival Outcomes and Variable Analyses\" paragraph 3", "quote": "Figure 2(c), the ROC curve found that TRIM28 was associated with prognosis since its AUC for survival prediction was 0.687."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "High TRIM28 expression was an independent predictor of poor prognosis in LIHC (P value <0.001), with an AUC of 0.687 for survival prediction.", "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:36238495"], "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:GSE14520"], "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:GSE14520"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36238495", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/6267851", "sha256": "sha256:0f5d92f328144d1f4b8603c6f24044e40058b6be0d3f10b8643e65255f90c53a", "bytes": 31346, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/6267851", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9553339", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14520", "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=GSE14520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14520", "version": null, "note": "The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to 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. The qRT-PCR data used to support the findings of this study have not been made available. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63898; and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87630).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to 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. The qRT-PCR data used to support the findings of this study have not been made available. 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The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to 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. The qRT-PCR data used to support the findings of this study have not been made available. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63898; and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87630).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to 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. The qRT-PCR data used to support the findings of this study have not been made available. 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and epidrivers in hepatocellular carcinoma", "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:GSE87630", "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=GSE87630", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87630", "version": null, "note": "The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to 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. The qRT-PCR data used to support the findings of this study have not been made available. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63898; and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87630).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to 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. The qRT-PCR data used to support the findings of this study have not been made available. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63898; and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87630).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2335922", "GSM2335923", "GSM2335924", "GSM2335925", "GSM2335926", "GSM2335927", "GSM2335928", "GSM2335929", "GSM2335930", "GSM2335931", "GSM2335932", "GSM2335933", "GSM2335934", "GSM2335935", "GSM2335936", "GSM2335937", "GSM2335938", "GSM2335939", "GSM2335940", "GSM2335941", "GSM2335942", "GSM2335943", "GSM2335944", "GSM2335945", "GSM2335946", "GSM2335947", "GSM2335948", "GSM2335949", "GSM2335950", "GSM2335951", "GSM2335952", "GSM2335953", "GSM2335954", "GSM2335955", "GSM2335956", "GSM2335957", "GSM2335958", "GSM2335959", "GSM2335960", "GSM2335961", "GSM2335962", "GSM2335963", "GSM2335964", "GSM2335965", "GSM2335966", "GSM2335967", "GSM2335968", "GSM2335969", "GSM2335970", "GSM2335971", "GSM2335972", "GSM2335973", "GSM2335974", "GSM2335975", "GSM2335976", "GSM2335977", "GSM2335978", "GSM2335979", "GSM2335980", "GSM2335981", "GSM2335982", "GSM2335983", "GSM2335984", "GSM2335985", "GSM2335986", "GSM2335987", "GSM2335988", "GSM2335989", "GSM2335990", "GSM2335991", "GSM2335992", "GSM2335993", "GSM2335994", "GSM2335995", "GSM2335996", "GSM2335997", "GSM2335998", "GSM2335999", "GSM2336000", "GSM2336001", "GSM2336002", "GSM2336003", "GSM2336004", "GSM2336005", "GSM2336006", "GSM2336007", "GSM2336008", "GSM2336009", "GSM2336010", "GSM2336011", "GSM2336012", "GSM2336013", "GSM2336014", "GSM2336015"], "sample_count": 94, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Integrated analysis of genomic and epigenomic regulation of transcriptome identifies molecular subtypes of liver cancer (gene expression)", "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:GSE14520 not downloaded", "asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE63898 not downloaded", "asset:data:geo:GSE63898 licence not read", "asset:data:geo:GSE87630 not downloaded", "asset:data:geo:GSE87630 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To summarize, survival analysis was performed by graphing K-M survival curves with the R packages survival and survminer. The K-M survival curve was used to compare the OS and progression-free interval (PFI) between the high and low TRIM28 groups."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Logistic regression"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "classification_metrics", "expected_value": 0.001, "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": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: roc."}, "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": ["GSE14520", "GSE63898", "GSE87630"], "resolved_accessions": ["GSE14520", "GSE63898", "GSE87630"], "statements": ["The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to 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. The qRT-PCR data used to support the findings of this study have not been made available. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63898; and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87630)."], "basis": "The paper names GSE14520, GSE63898, GSE87630 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": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "assets": ["source:pmid:36238495", "data:geo:GSE14520"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14520"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:10:46Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9387, "completion_tokens": 1922, "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:36238495", "type": "paper", "label": "pmid:36238495"}, {"id": "source:pmid:36238495", "type": "manuscript", "label": "PMID 36238495 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36238495", "type": "paper", "label": "pmid:36238495"}, {"id": "source:pmid:36238495", "type": "manuscript", "label": "PMID 36238495 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36238495", "type": "extraction", "used": ["source:pmid:36238495"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14520", "type": "accession_resolution", "used": ["data:geo:GSE14520"], "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:36238495", "parent_hash": "sha256:2cdc95a27bf035c95047293f28eaddb5128a0c0b16af39d0e87071ea2798eae3", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE63898 licence not read", "asset:data:geo:GSE63898 not downloaded", "asset:data:geo:GSE87630 licence not read", "asset:data:geo:GSE87630 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": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ere validated using GEPIA, ROC analysis, and immunohistochemical staining pictures from the THPA. GSE14520, G"], "order_basis": "paper_text_order:1058", "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": 0.77, "evidence": ["y the authenticity of cell lines. Cells were cultured in Dulbecco's modified Eagle's medium (DMEM) su"], "order_basis": "paper_text_order:2360", "id": "assay:2"}, {"role": "analysis", "definition_id": "diagnostic_evaluation", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["To summarize, survival analysis was performed by graphing K-M survival curves with the R packages survival and survminer. The K-M survival curve was used to compare the OS and progression-free interval (PFI) between the high and low TRIM28 groups."], "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":"2026-11-04T02:22:37+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}}}