{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38097783", "kind": "science-record", "revision": 3, "content_hash": "sha256:f751d218f8c05c1a3b10703a8a296877b6a5387de3147700d7721a0ce44d283b", "created_at": "2026-11-01T19:03:02Z", "updated_at": "2026-11-01T21:32:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics-based analysis of the relationship between disulfidptosis and prognosis and treatment response in pancreatic cancer.", "doi": "10.1038/s41598-023-49752-4", "pmid": "38097783", "authors": ["Yuanpeng Xiong", "Xiaoyu Kong", "Haoran Mei", "Jie Wang", "Shifa Zhou"], "journal": "Scientific reports", "year": 2023, "abstract": "Tumor formation is closely associated with disulfidptosis, a new form of cell death induced by disulfide stress-induced. The exact mechanism of action of disulfidptosis in pancreatic cancer (PCa) is not clear. This study analyzed the impact of disulfidptosis-related genes (DRGs) on the prognosis of PCa and identified clusters of DRGs, and based on this, a risk score (RS) signature was developed to assess the impact of RS on the prognosis, immune and chemotherapeutic response of PCa patients. Based on transcriptomic data and clinical information from PCa tissue and normal pancreatic tissue samples obtained from the TCGA and GTEx databases, differentially expressed and differentially surviving DRGs in PCa were identified from among 15 DRGs. Two DRGs clusters were identified by consensus clustering by merging the PCa samples in the GSE183795 dataset. Analysis of DRGs clusters about the PCa tumor microenvironment and differential analysis to obtain differential genes between the two DRG clusters. Patients were then randomized into the training and testing sets, and a prognostic prediction signature associated with disulfidptosis was constructed in the training set. Then all samples were divided into high-disulfidptosis-risk (HDR) and low-disulfidptosis-risk (LDR) subgroups based on the RS calculated from the signature. The predictive efficacy of the signature was assessed by survival analysis, nomograms, correlation analysis of clinicopathological characteristics, and the receiver operating characteristic (ROC) curves. To assess differences between different risk subgroups in immune cell infiltration, expression of immune checkpoint molecules, somatic gene mutations, and effectiveness of immunotherapy and chemotherapy. The GSE57495 dataset was used as external validation, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression levels of DRGs. A total of 12 DRGs with differential expression and prognosis in PCa were identified, based on which a risk-prognosis signature containing five differentially expressed genes (DEGs) was developed. The signature was a good predictor and an independent risk factor. The nomogram and calibration curve shows the signature's excellent clinical applicability. Functional enrichment analysis showed that RS was associated with tumor and immune-related pathways. RS was strongly associated with the tumor microenvironment, and analysis of response to immunotherapy and chemotherapy suggests that the signature can be used to assess the sensitivity of treatments. External validation further demonstrated the model's efficacy in predicting the prognosis of PCa patients, with RT-qPCR and immunohistochemical maps visualizing the expression of each gene in PCa cell lines and the tissue. Our study is the first to apply the subtyping model of disulfidptosis to PCa and construct a signature based on the disulfidptosis subtype, which can provide an accurate assessment of prognosis, immunotherapy, and chemotherapy response in PCa patients, providing new targets and directions for the prognosis and treatment of PCa.", "claims": [{"id": "claim-method", "statement": "Subsequently, we constructed the prognostic risk signature associated with disulfidptosis using Lasso and multivariate Cox (Lasso–Cox) regression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38097783", "locator": "sections[7] \"Identification of differentially expressed genes (DEGs) of the disulfidptosis subtypes and the establishment of a prognostic signature\" paragraph 2", "quote": "Subsequently, we constructed the prognostic risk signature associated with disulfidptosis using Lasso and multivariate Cox (Lasso–Cox) regression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38097783", "locator": "sections[34] \"notes\" paragraph 1", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 12 DRGs with differential expression and prognosis in PCa were identified, based on which a risk-prognosis signature containing five differentially expressed genes (DEGs) was developed.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38097783", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 12 DRGs with differential expression and prognosis in PCa were identified, based on which a risk-prognosis signature containing five differentially expressed genes (DEGs) was developed."}, {"asset": "source:pmid:38097783", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The signature was a good predictor and an independent risk factor."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 12 DRGs with differential expression and prognosis in PCa were identified, based on which a risk-prognosis signature containing five differentially expressed genes (DEGs) was developed.", "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:38097783"], "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:GSE183795"], "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:GSE183795"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38097783", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-023-49752-4", "sha256": "sha256:db1906637249e725dcab6f333aff7cd6fdd0c512749b28574654afb082d93e2e", "bytes": 40972, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-023-49752-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10721597", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE183795", "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=GSE183795", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE183795", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5570968", "GSM5570969", "GSM5570970", "GSM5570971", "GSM5570972", "GSM5570973", "GSM5570974", "GSM5570975", "GSM5570976", "GSM5570977", "GSM5570978", "GSM5570979", "GSM5570980", "GSM5570981", "GSM5570982", "GSM5570983", "GSM5570984", "GSM5570985", "GSM5570986", "GSM5570987", "GSM5570988", "GSM5570989", "GSM5570990", "GSM5570991", "GSM5570992", "GSM5570993", "GSM5570994", "GSM5570995", "GSM5570996", "GSM5570997", "GSM5570998", "GSM5570999", "GSM5571000", "GSM5571001", "GSM5571002", "GSM5571003", "GSM5571004", "GSM5571005", "GSM5571006", "GSM5571007", "GSM5571008", "GSM5571009", "GSM5571010", "GSM5571011", "GSM5571012", "GSM5571013", "GSM5571014", "GSM5571015", "GSM5571016", "GSM5571017", "GSM5571018", "GSM5571019", "GSM5571020", "GSM5571021", "GSM5571022", "GSM5571023", "GSM5571024", "GSM5571025", "GSM5571026", "GSM5571027", "GSM5571028", "GSM5571029", "GSM5571030", "GSM5571031", "GSM5571032", "GSM5571033", "GSM5571034", "GSM5571035", "GSM5571036", "GSM5571037", "GSM5571038", "GSM5571039", "GSM5571040", "GSM5571041", "GSM5571042", "GSM5571043", "GSM5571044", "GSM5571045", "GSM5571046", "GSM5571047", "GSM5571048", "GSM5571049", "GSM5571050", "GSM5571051", "GSM5571052", "GSM5571053", "GSM5571054", "GSM5571055", "GSM5571056", "GSM5571057", "GSM5571058", "GSM5571059", "GSM5571060", "GSM5571061", "GSM5571062", "GSM5571063", "GSM5571064", "GSM5571065", "GSM5571066", "GSM5571067", "GSM5571068", "GSM5571069", "GSM5571070", "GSM5571071", "GSM5571072", "GSM5571073", "GSM5571074", "GSM5571075", "GSM5571076", "GSM5571077", "GSM5571078", "GSM5571079", "GSM5571080", "GSM5571081", "GSM5571082", "GSM5571083", "GSM5571084", "GSM5571085", "GSM5571086", "GSM5571087", "GSM5571088", "GSM5571089", "GSM5571090", "GSM5571091", "GSM5571092", "GSM5571093", "GSM5571094", "GSM5571095", "GSM5571096", "GSM5571097", "GSM5571098", "GSM5571099", "GSM5571100", "GSM5571101", "GSM5571102", "GSM5571103", "GSM5571104", "GSM5571105", "GSM5571106", "GSM5571107", "GSM5571108", "GSM5571109", "GSM5571110", "GSM5571111", "GSM5571112", "GSM5571113", "GSM5571114", "GSM5571115", "GSM5571116", "GSM5571117", "GSM5571118", "GSM5571119", "GSM5571120", "GSM5571121", "GSM5571122", "GSM5571123", "GSM5571124", "GSM5571125", "GSM5571126", "GSM5571127", "GSM5571128", "GSM5571129", "GSM5571130", "GSM5571131", "GSM5571132", "GSM5571133", "GSM5571134", "GSM5571135", "GSM5571136", "GSM5571137", "GSM5571138", "GSM5571139", "GSM5571140", "GSM5571141", "GSM5571142", "GSM5571143", "GSM5571144", "GSM5571145", "GSM5571146", "GSM5571147", "GSM5571148", "GSM5571149", "GSM5571150", "GSM5571151", "GSM5571152", "GSM5571153", "GSM5571154", "GSM5571155", "GSM5571156", "GSM5571157", "GSM5571158", "GSM5571159", "GSM5571160", "GSM5571161", "GSM5571162", "GSM5571163", "GSM5571164", "GSM5571165", "GSM5571166", "GSM5571167", "GSM5571168", "GSM5571169", "GSM5571170", "GSM5571171", "GSM5571172", "GSM5571173", "GSM5571174", "GSM5571175", "GSM5571176", "GSM5571177", "GSM5571178", "GSM5571179", "GSM5571180", "GSM5571181", "GSM5571182", "GSM5571183", "GSM5571184", "GSM5571185", "GSM5571186", "GSM5571187", "GSM5571188", "GSM5571189", "GSM5571190", "GSM5571191", "GSM5571192", "GSM5571193", "GSM5571194", "GSM5571195", "GSM5571196", "GSM5571197", "GSM5571198", "GSM5571199", "GSM5571200", "GSM5571201", "GSM5571202", "GSM5571203", "GSM5571204", "GSM5571205", "GSM5571206", "GSM5571207", "GSM5571208", "GSM5571209", "GSM5571210", "GSM5571211"], "sample_count": 244, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Microarray gene-expression profiles of 139 pancreatic tumor,102 adjacent non-tumor tissue  from patients with pancreatic ductal adenocarcinoma  and 3 normal pancreas from donors.", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE57495", "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=GSE57495", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57495", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1383778", "GSM1383779", "GSM1383780", "GSM1383781", "GSM1383782", "GSM1383783", "GSM1383784", "GSM1383785", "GSM1383786", "GSM1383787", "GSM1383788", "GSM1383789", "GSM1383790", "GSM1383791", "GSM1383792", "GSM1383793", "GSM1383794", "GSM1383795", "GSM1383796", "GSM1383797", "GSM1383798", "GSM1383799", "GSM1383800", "GSM1383801", "GSM1383802", "GSM1383803", "GSM1383804", "GSM1383805", "GSM1383806", "GSM1383807", "GSM1383808", "GSM1383809", "GSM1383810", "GSM1383811", "GSM1383812", "GSM1383813", "GSM1383814", "GSM1383815", "GSM1383816", "GSM1383817", "GSM1383818", "GSM1383819", "GSM1383820", "GSM1383821", "GSM1383822", "GSM1383823", "GSM1383824", "GSM1383825", "GSM1383826", "GSM1383827", "GSM1383828", "GSM1383829", "GSM1383830", "GSM1383831", "GSM1383832", "GSM1383833", "GSM1383834", "GSM1383835", "GSM1383836", "GSM1383837", "GSM1383838", "GSM1383839", "GSM1383840"], "sample_count": 63, "group_sizes": null, "group_sizes_basis": null, "platform": "15048", "taxon": "Homo sapiens", "title": "Development of a prognostic gene signature in pancreatic cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE183795 not downloaded", "asset:data:geo:GSE183795 licence not read", "asset:data:geo:GSE57495 not downloaded", "asset:data:geo:GSE57495 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}, {"id": "method-2", "family": null, "specific": null, "label": "Lasso and multivariate Cox (Lasso–Cox) regression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Subsequently, we constructed the prognostic risk signature associated with disulfidptosis using Lasso and multivariate Cox (Lasso–Cox) regression analysis."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "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": ["GSE183795", "GSE57495"], "resolved_accessions": ["GSE183795", "GSE57495"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE183795, GSE57495 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pca_fit"], "assets": ["source:pmid:38097783", "data:geo:GSE183795"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE183795"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:02:48Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11437, "completion_tokens": 2494, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38097783", "type": "paper", "label": "pmid:38097783"}, {"id": "source:pmid:38097783", "type": "manuscript", "label": "PMID 38097783 full text"}, {"id": "data:geo:GSE183795", "type": "dataset", "label": "GEO GSE183795"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38097783", "type": "paper", "label": "pmid:38097783"}, {"id": "source:pmid:38097783", "type": "manuscript", "label": "PMID 38097783 full text"}, {"id": "data:geo:GSE183795", "type": "dataset", "label": "GEO GSE183795"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38097783", "type": "extraction", "used": ["source:pmid:38097783"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE183795", "type": "accession_resolution", "used": ["data:geo:GSE183795"], "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:38097783", "parent_hash": "sha256:bd682c5fed92a44c50611aae660a2cac0b48a1573852d0893d7248fe1c67093e", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE183795 licence not read", "asset:data:geo:GSE183795 not downloaded", "asset:data:geo:GSE57495 licence not read", "asset:data:geo:GSE57495 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tion-quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression levels of", "edicting the prognosis of PCa patients, with RT-qPCR and immunohistochemical maps visualizing the", "n-quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression levels of", "cting the prognosis of PCa patients, with RT-qPCR and immunohistochemical maps visualizing the"], "order_basis": "paper_text_order:1948", "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": 0.93, "evidence": ["prognosis of PCa patients, with RT-qPCR and immunohistochemical maps visualizing the expression of each gene"], "order_basis": "paper_text_order:2788", "id": "assay:2"}, {"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["PCA"], "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":"2026-11-04T02:54:06+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}}}