{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35836112", "kind": "science-record", "revision": 4, "content_hash": "sha256:c3e31c26a6fcaaeff3fc798dd72f1d8703f834cca82a7e26f6e82eec4a39e50e", "created_at": "2026-11-01T18:14:54Z", "updated_at": "2026-11-01T22:07:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The novel transcriptomic signature of angiogenesis predicts clinical outcome, tumor microenvironment and treatment response for prostate adenocarcinoma.", "doi": "10.1186/s10020-022-00504-6", "pmid": "35836112", "authors": ["Cheng-Yuan Gu", "Bo Dai", "Yao Zhu", "Guo-Wen Lin", "Hong-Kai Wang", "Ding-Wei Ye", "Xiao-Jian Qin"], "journal": "Molecular medicine (Cambridge, Mass.)", "year": 2022, "abstract": "Angiogenesis plays the critical roles in promoting tumor progression, aggressiveness, and metastasis. Although few studies have revealed some angiogenesis-related genes (ARGs) could serve as prognosis-related biomarkers for the prostate cancer (PCa), the integrated role of ARGs has not been systematically studied. The RNA-sequencing data and clinical information of prostate adenocarcinoma (PRAD) were downloaded from The Cancer Genome Atlas (TCGA) as discovery dataset. Twenty-three ARGs in total were identified to be correlated with prognosis of PRAD by the univariate Cox regression analysis, and a 19-ARG signature was further developed with significant correlation with the disease-free survival (DFS) of PRAD by the least absolute shrinkage and selection operator (LASSO) Cox regression with tenfold cross-validation. The signature stratified PRAD patients into high- and low-ARGs signature score groups, and those with high ARGs signature score were associated with significantly poorer outcomes (median DFS: 62.71 months vs unreached, p < 0.0001). The predicting ability of ARGs signature was subsequently validated in two independent cohorts of GSE40272 & PRAD_MSKCC. Notably, the 19-ARG signature outperformed the typical clinical features or each involved ARG in predicting the DFS of PRAD. Furthermore, a prognostic nomogram was constructed with three independent prognostic factors, including the ARGs signature, T stage and Gleason score. The predicted results from the nomogram (C-index = 0.799, 95%CI = 0.744-0.854) matched well with the observed outcomes, which was verified by the calibration curves. The values of area under receiver operating characteristic curve (AUC) for DFS at 1-, 3-, 5-year for the nomogram were 0.82, 0.83, and 0.83, respectively, indicating the performance of nomogram model is of reasonably high accuracy and robustness. Moreover, functional enrichment analysis demonstrated the potential targets of E2F targets, G2M checkpoint pathways, and cell cycle pathways to suppress the PRAD progression. Of note, the high-risk PRAD patients were more sensitive to immune therapies, but Treg might hinder benefits from immunotherapies. Additionally, this established tool also could predict response to neoadjuvant androgen deprivation therapy (ADT) and some chemotherapy drugs, such as cisplatin, paclitaxel, and docetaxel, etc. The novel ARGs signature, with prognostic significance, can further promote the application of targeted therapies in different stratifications of PCa patients.", "claims": [{"id": "claim-method", "statement": "The ARGs related to DFS (P < 0.05) were identified via a univariate Cox regression analysis using optimized algorithm. Following least absolute shrinkage and selection operator (LASSO) Cox regression with tenfold cross-validation was performed using the “glmnet” package in R studio (Sauerbrei et al. 2007; Wang et al. 2019). Multivariate Cox regression analysis was then conducted for the construction of this ARG signature, and the ARGs signature score formula was established.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35836112", "locator": "sections[5] \"Construction of the angiogenesis-related prognostic signature and nomogram\" paragraph 2", "quote": "The ARGs related to DFS (P < 0.05) were identified via a univariate Cox regression analysis using optimized algorithm. Following least absolute shrinkage and selection operator (LASSO) Cox regression with tenfold cross-validation was performed using the “glmnet” package in R studio (Sauerbrei et al. 2007; Wang et al. 2019). Multivariate Cox regression analysis was then conducted for the construction of this ARG signature, and the ARGs signature score formula was established."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed in the present study was from the public database. The data can be downloaded from: https://www.cbioportal.org/study/summary?id=prad_tcga, https://gdc-hub.s3.us-east-1.amazonaws.com/download/TCGA-PRAD.htseq_counts.tsv.gz, https://www.ncbi.nlm.nih.gov/geo/, http://www.gsea-msigdb.org/gsea/msigdb/, https://www.cancerrxgene.org/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35836112", "locator": "sections[30] \"notes\" paragraph 1", "quote": "The datasets analyzed in the present study was from the public database. The data can be downloaded from: https://www.cbioportal.org/study/summary?id=prad_tcga, https://gdc-hub.s3.us-east-1.amazonaws.com/download/TCGA-PRAD.htseq_counts.tsv.gz, https://www.ncbi.nlm.nih.gov/geo/, http://www.gsea-msigdb.org/gsea/msigdb/, https://www.cancerrxgene.org/."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The 19-ARG signature outperformed the typical clinical features or each involved ARG in predicting the DFS of PRAD.", "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:35836112"], "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:GSE102124"], "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:GSE102124"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35836112", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s10020-022-00504-6", "sha256": "sha256:61ec780d58e9077aa83d0944c9d274512923e6519fbced70d0a69d0bad867e5e", "bytes": 54478, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s10020-022-00504-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9284787", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102124", "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=GSE102124", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102124", "version": null, "note": "The datasets analyzed in the present study was from the public database. 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The data can be downloaded from: https://www.cbioportal.org/study/summary?id=prad_tcga, https://gdc-hub.s3.us-east-1.amazonaws.com/download/TCGA-PRAD.htseq_counts.tsv.gz, https://www.ncbi.nlm.nih.gov/geo/, http://www.gsea-msigdb.org/gsea/msigdb/, https://www.cancerrxgene.org/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2724470", "GSM2724471", "GSM2724472", "GSM2724473", "GSM2724474", "GSM2724475", "GSM2724476", "GSM2724477", "GSM2724478", "GSM2724479", "GSM2724480", "GSM2724481", "GSM2724482", "GSM2724483", "GSM2724484", "GSM2724485", "GSM2724486", "GSM2724487", "GSM2724488", "GSM2724489", "GSM2724490", "GSM2724491"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "17586", "taxon": "Homo sapiens", "title": "Gene expression profiling of treated and untreated primary prostate cancer", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE140440", "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=GSE140440", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE140440", "version": null, "note": "The datasets analyzed in the present study was from the public database. 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The data can be downloaded from: https://www.cbioportal.org/study/summary?id=prad_tcga, https://gdc-hub.s3.us-east-1.amazonaws.com/download/TCGA-PRAD.htseq_counts.tsv.gz, https://www.ncbi.nlm.nih.gov/geo/, http://www.gsea-msigdb.org/gsea/msigdb/, https://www.cancerrxgene.org/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1616614", "GSM1616615", "GSM1616616", "GSM1616617", "GSM1616618", "GSM1616619", "GSM1616620", "GSM1616621", "GSM1616622", "GSM1616623", "GSM1616624", "GSM1616625", "GSM1616626", "GSM1616627", "GSM1616628", "GSM1616629", "GSM1616630", "GSM1616631", "GSM1616632", "GSM1616633", "GSM1616634", "GSM1616635", "GSM1616636", "GSM1616637", "GSM1616638", "GSM1616639", "GSM1616640", "GSM1616641", "GSM1616642", "GSM1616643", "GSM1616644", "GSM1616645", "GSM1616646", "GSM1616647", "GSM1616648", "GSM1616649", "GSM1616650", "GSM1616651", "GSM1616652", "GSM1616653", "GSM1616654", "GSM1616655", "GSM1616656", "GSM1616657", "GSM1616658", "GSM1616659", "GSM1616660", "GSM1616661", "GSM1616662", "GSM1616663", "GSM1616664", "GSM1616665", "GSM1616666", "GSM1616667", "GSM1616668", "GSM1616669", "GSM1616670", "GSM1616671", "GSM1616672", "GSM1616673", "GSM1616674", "GSM1616675", "GSM1616676", "GSM1616677", "GSM1616678", "GSM1616679", "GSM1616680", "GSM1616681", "GSM1616682", "GSM1616683", "GSM1616684", "GSM1918978", "GSM1918979", "GSM1918980", "GSM1930063", "GSM1930065", "GSM1930066", "GSM1930068", "GSM1930069", "GSM1930071", "GSM1930072", "GSM1930074", "GSM1930075", "GSM1930076", "GSM1930077", "GSM1930078", "GSM1930079", "GSM1930080", "GSM1930081", "GSM1930082", "GSM1930083", "GSM1930084", "GSM1930086", "GSM1930089", "GSM1930090", "GSM1930091", "GSM1930093", "GSM1930094", "GSM1930095", "GSM1930096", "GSM1930097", "GSM1930101", "GSM1930102", "GSM1930104", "GSM1930105", "GSM1930106", "GSM1930107", "GSM1930108", "GSM1930109", "GSM1930111", "GSM1930112", "GSM1930113", "GSM1930114", "GSM1930115", "GSM1930117", "GSM1930118", "GSM1930119", "GSM1930121", "GSM1930122", "GSM1930123", "GSM1930124", "GSM1930125", "GSM1930127", "GSM1930128", "GSM1930129", "GSM1930130", "GSM1930131", "GSM1930132", "GSM1930133", "GSM1930134", "GSM1930135", "GSM1930136", "GSM1930137", "GSM1930139", "GSM1930141", "GSM1930142", "GSM1930143", "GSM1930146", "GSM1930147", "GSM1930148", "GSM1930149", "GSM1930150", "GSM1930152", "GSM1930153", "GSM1930155", "GSM1930156", "GSM1930157", "GSM1930158", "GSM1930159"], "sample_count": 149, "group_sizes": null, "group_sizes_basis": null, "platform": "15659", "taxon": "Homo sapiens", "title": "Epithelial mesenchymal-like transition occurs in a subset of cells in castration resistant prostate cancer bone metastases", "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:GSE102124 not downloaded", "asset:data:geo:GSE102124 licence not read", "asset:data:geo:GSE140440 not downloaded", "asset:data:geo:GSE140440 licence not read", "asset:data:geo:GSE40272 not downloaded", "asset:data:geo:GSE40272 licence not read", "asset:data:geo:GSE74685 not downloaded", "asset:data:geo:GSE74685 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The ARGs related to DFS (P < 0.05) were identified via a univariate Cox regression analysis using optimized algorithm. Following least absolute shrinkage and selection operator (LASSO) Cox regression with tenfold cross-validation was performed using the “glmnet” package in R studio (Sauerbrei et al. 2007; Wang et al. 2019). Multivariate Cox regression analysis was then conducted for the construction of this ARG signature, and the ARGs signature score formula was established."}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-3", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fold_change": "” package, while |log2 (Fold Change) |> 1 and p < 0"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "DeSeq2"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["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": ["GSE40272", "GSE102124", "GSE74685", "GSE140440"], "resolved_accessions": ["GSE40272", "GSE102124", "GSE74685", "GSE140440"], "statements": ["The datasets analyzed in the present study was from the public database. The data can be downloaded from: https://www.cbioportal.org/study/summary?id=prad_tcga, https://gdc-hub.s3.us-east-1.amazonaws.com/download/TCGA-PRAD.htseq_counts.tsv.gz, https://www.ncbi.nlm.nih.gov/geo/, http://www.gsea-msigdb.org/gsea/msigdb/, https://www.cancerrxgene.org/."], "basis": "The paper names GSE40272, GSE102124, GSE74685, GSE140440 in 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:35836112", "data:geo:GSE102124"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102124"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:55:25Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15445, "completion_tokens": 3452, "cached_tokens": 188}}, "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:35836112", "type": "paper", "label": "pmid:35836112"}, {"id": "source:pmid:35836112", "type": "manuscript", "label": "PMID 35836112 full text"}, {"id": "data:geo:GSE102124", "type": "dataset", "label": "GEO GSE102124"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35836112", "type": "paper", "label": "pmid:35836112"}, {"id": "source:pmid:35836112", "type": "manuscript", "label": "PMID 35836112 full text"}, {"id": "data:geo:GSE102124", "type": "dataset", "label": "GEO GSE102124"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35836112", "type": "extraction", "used": ["source:pmid:35836112"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102124", "type": "accession_resolution", "used": ["data:geo:GSE102124"], "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:35836112", "parent_hash": "sha256:ced7c4ed67390a1c72780083738e3d98603c751170045258aba032bf52f6ebfe", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE102124 licence not read", "asset:data:geo:GSE102124 not downloaded", "asset:data:geo:GSE140440 licence not read", "asset:data:geo:GSE140440 not downloaded", "asset:data:geo:GSE40272 licence not read", "asset:data:geo:GSE40272 not downloaded", "asset:data:geo:GSE74685 licence not read", "asset:data:geo:GSE74685 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["The novel transcriptomic signature of angiogenesis predicts clinical", "RGs has not been systematically studied. The RNA-sequencing data and clinical information of prostate ad"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tein expression was not estimated.Fig. 11The immunohistochemistry (IHC) analysis. A The collection of IHC stai", "0.76, 0.68 and 0.63, respectively (Fig. 3H). IHC analysis of ARGs protein expression in human", "pression in human PRAD samples Additionally, IHC data were retrieved from the HPA database to", "ated in the cytoplasm and/or membrane by the IHC analysis (Fig. 11B). Whereas, COL3A1, PF4, P"], "order_basis": "paper_text_order:9517", "id": "assay:2"}, {"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": ["The ARGs related to DFS (P < 0.05) were identified via a univariate Cox regression analysis using optimized algorithm. Following least absolute shrinkage and selection operator (LASSO) Cox regression with tenfold cross-validation was performed using the “glmnet” package in R studio (Sauerbrei et al. 2007; Wang et al. 2019). Multivariate Cox regression analysis was then conducted for the construction of this ARG signature, and the ARGs signature score formula was established."], "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":"2026-11-04T00:31:57+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}}}