{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39248068", "kind": "science-record", "revision": 2, "content_hash": "sha256:b32bb58f5ffa8ca62932473f850bfb6708b4e2a1d42a1b63193112b5456ca38e", "created_at": "2026-11-01T10:25:48Z", "updated_at": "2026-11-01T14:01:32Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Bioinformatics Analysis Screening and Identification of Key Biomarkers and Drug Targets in Human Glioblastoma.", "doi": "10.2174/0109298673316883240829073901", "pmid": "39248068", "authors": null, "journal": "Current medicinal chemistry", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 88.0, "unit": "degs", "tolerance": null, "source": "chars 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"reader_status": "available", "identifier": "section[9]/table-wrap[2]#T2", "version": null, "note": "Molecular function (MF) pathway enrichment analysis of differentially expressed genes (DEGs) in glioblastoma.", "structure": {"pmcid": "PMC12606603", "section_index": 9, "section_title": "KEGG and GO Enrichment Analyses of DEGs", "row_count": 11, "column_count": 4}, "table": {"label": "Table 2", "caption": "Molecular function (MF) pathway enrichment analysis of differentially expressed genes (DEGs) in glioblastoma.", "rows": [["Term", "Pathway Description", "Count", "p-Value"], ["GO:0005871", "Kinesin complex", "6", "4.77E-06"], ["GO:0005876", "Spindle microtubule", "5", "2.36E-05"], ["GO:0030496", "Midbody", "6", "6.53E-05"], ["GO:0005581", "Collagen trimer", "5", "7.07E-05"], ["GO:0005874", "Microtubule", "5", "0.002346848"], ["GO:0051233", "Spindle midzone", "3", "0.003188572"], ["GO:0016328", "Lateral plasma membrane", "3", "0.013235985"], ["GO:0000796", "Condensin complex", "2", "0.021099162"], ["GO:0042383", "Sarcolemma", "3", "0.022842198"], ["GO:0005737", "Cytoplasm", "22", "0.022951589"]], "row_count": 11, "column_count": 4, "numeric_cells": 30, "header_rows": 1, "locator": "section[9]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:39248068:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:27e684c3ef085707f30b0654d4d2d187c5403092956ad700e32d0a6a10d6309f", "bytes": 880, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[3]#T3", "version": null, "note": "Changes in cell component (CC) pathway enrichment analysis of differentially expressed genes (DEGs) in glioblastoma.", "structure": {"pmcid": "PMC12606603", "section_index": 9, "section_title": "KEGG and GO Enrichment Analyses of DEGs", "row_count": 12, "column_count": 4}, "table": {"label": "Table 3", "caption": "Changes in cell component (CC) pathway enrichment analysis of differentially expressed genes (DEGs) in glioblastoma.", "rows": [["Term", "Description", "Count in Gene Set", "p-value"], ["cfa04510:", "Focal adhesion", "6", "0.003963"], ["cfa04151:", "PI3K-Akt signaling pathway", "7", "0.007034"], ["cfa04974:", "Protein digestion and absorption", "4", "0.009134"], ["cfa04512:", "ECM-receptor interaction", "4", "0.010054"], ["cfa05146:", "Amoebiasis", "4", "0.017115"], ["cfa05205:", "Proteoglycans in cancer", "5", "0.017563"], ["cfa04114:", "Oocyte meiosis", "4", "0.017985"], ["cfa04110:", "Cell cycle", "4", "0.025292"], ["cfa05206:", "MicroRNAs in cancer", "4", "0.034612"], ["cfa04115:", "p53 signaling pathway", "3", "0.044317"], ["cfa05200:", "Pathways in cancer", "6", "0.048794"]], "row_count": 12, "column_count": 4, "numeric_cells": 34, "header_rows": 1, "locator": "section[9]/table-wrap[3]#T3"}}, {"id": "asset:table:pmid:39248068:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:07d9dade77d8ed6c52afc1821c6d708be9a423462b5a847667802ca24a6e51ff", "bytes": 814, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[4]#T4", "version": null, "note": "Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes (DEGs) in glioblastoma.", "structure": {"pmcid": "PMC12606603", "section_index": 9, "section_title": "KEGG and GO Enrichment Analyses of DEGs", "row_count": 9, "column_count": 4}, "table": {"label": "Table 4", "caption": "Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes (DEGs) in glioblastoma.", "rows": [["Term", "Pathway Description", "Count", "p-value"], ["GO:0003777", "Microtubule motor activity", "5", "2.36E-04"], ["GO:0005201", "Extracellular matrix structural constituent", "4", "9.42E-04"], ["GO:0016887", "ATPase activity", "5", "0.001533"], ["GO:0005524", "ATP binding", "14", "0.005736"], ["GO:0035174", "Histone serine kinase activity", "2", "0.025983"], ["GO:0004871", "Signal transducer activity", "4", "0.026153"], ["GO:0005200", "Structural constituent of cytoskeleton", "3", "0.028268"], ["GO:0004859", "Phospholipase inhibitor activity", "2", "0.031099"]], "row_count": 9, "column_count": 4, "numeric_cells": 24, "header_rows": 1, "locator": "section[9]/table-wrap[4]#T4"}}, {"id": "asset:table:pmid:39248068:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a9dbe32eb4ce1e52a2ba606676c3958b70e0cc35417ac2985fc5e793d4b95077", "bytes": 4946, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T5", "version": null, "note": "Functional roles of 27 hub genes with degree-10.", "structure": {"pmcid": "PMC12606603", "section_index": 11, "section_title": "Hub Gene Selection and Analysis", "row_count": 28, "column_count": 3}, "table": {"label": "Table 5", "caption": "Functional roles of 27 hub genes with degree-10.", "rows": [["Gene Symbol", "Full Name", "Function"], ["GINS1", "DNA replication complex GINS protein PSF1", "The GINS complex plays an essential role in the initiation of DNA replication, and progression of DNA replication forks."], ["SKA1", "Spindle and kinetochore-associated protein 1", "Component of the SKA1 complex, a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation."], ["BUB1B", "Mitotic checkpoint serine/threonine-protein kinase BUB1 beta", "Essential component of the mitotic checkpoint. Required for normal mitosis progression."], ["CCNB2", "G2/mitotic-specific cyclin-B2", "CCNB2 (cyclin B2) is associated with invasion, metastasis and poor prognosis of several cancers."], ["MELK", "Maternal embryonic leucine zipper kinase", "Serine/threonine-protein kinase involved in various processes such as cell cycle regulation, self-renewal of stem cells, apoptosis and splicing regulation."], ["KIAA0101", "PCNA-associated factor", "PCNA-binding protein that acts as a regulator of DNA repair during DNA replication."], ["SHCBP1", "SHC SH2 domain-binding protein 1", "May play a role in signaling pathways governing cellular proliferation, cell growth and differentiation."], ["AURKB", "Aurora kinase B", "Serine/threonine-protein kinase component of the chromosomal passenger complex (CPC), a complex that acts as a key regulator of mitosis."], ["EZH2", "Histone-lysine N-methyltransferase EZH2", "Catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys- 27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene."], ["KNTC1", "Kinetochore-associated protein 1", "Essential component of the mitotic checkpoint, which prevents cells from prematurely exiting mitosis."], ["SMC4", "Structural maintenance of chromosomes protein 4", "Central component of the condensin complex, a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes."], ["RRM2", "Ribonucleoside-diphosphate reductase subunit M2", "Provides the precursors necessary for DNA synthesis."], ["KIF14", "Kinesin-like protein KIF14", "Microtubule motor protein that binds to microtubules with high affinity through each tubulin heterodimer and has an ATPase activity (By similarity)."], ["LMNB1", "Lamin-B1", "Lamins are components of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane, which is thought to provide a framework for the nuclear envelope and may also interact with chromatin."], ["CENPN", "Centromere protein N", "Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation."], ["KIFC1", "Kinesin-like protein KIFC1", "Minus end-directed microtubule-dependent motor required for bipolar spindle formation."], ["KIF20A", "Kinesin-like protein KIF20A", "Mitotic kinesin required for chromosome passenger complex (CPC)-mediated cytokinesis."], ["CEP55", "Centrosomal protein of 55 kDa", "Plays a role in mitotic exit and cytokinesis."], ["TOP2A", "Topoisomerase(DNA)II ɑ", "Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands."], ["NUSAP1", "Nucleolar and spindle associated protein 1", "High expression of NUSAP1 is involved in the progression of prostate cancer."], ["CDK1", "Cyclin-dependent kinase 1", "Plays a key role in the control of the eukaryotic cell cycle by modulating the centrosome cycle as well as mitotic onset."], ["ASPM", "Abnormal spindle-like microcephaly-associated protein", "The function in regulating microtubule dynamics at spindle poles including spindle orientation, astral microtubule density and poleward microtubule flux seems to depend on the association with the katanin complex formed by KATNA1 and KATNB1."], ["AURKA", "Aurora kinase A", "Mitotic serine/threonine kinase that contributes to the regulation of cell cycle progression."], ["NCAPG", "Activation of CDK1 at centrosomes", "Regulatory subunit of the condensin complex, a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes."], ["GINS2", "DNA replication complex GINS protein PSF2", "The GINS complex plays an essential role in the initiation of DNA replication, and progression of DNA replication forks."], ["KIF23", "Kinesin-like protein KIF23", "Component of the centralspindlin complex that serves as a microtubule-dependent and Rho-mediated signaling required for the myosin contractile ring formation during the cell cycle cytokinesis."], ["NDC80", "Kinetochore protein NDC80 homolog", "Acts as a component of the essential kinetochore- associated NDC80 complex, which is required for chromosome segregation and spindle checkpoint activity."]], "row_count": 28, "column_count": 3, "numeric_cells": 19, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T5"}}, {"id": "asset:table:pmid:39248068:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fed30ad285e2a858745b5b1d4fdc1acec7f15c859d2352f0277cac27440be4dd", "bytes": 890, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#T6", "version": null, "note": "Biological processes (BP) pathway enrichment analysis of hub genes in glioblastoma.", "structure": {"pmcid": "PMC12606603", "section_index": 11, "section_title": "Hub Gene 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"raw_response": "{\"parent_value\":88,\"unit\":\"DEGs\",\"evidence\":\"The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.\",\"target_result\":\"The paper reports that the analysis identified 88 differentially expressed genes.\",\"number_stated\":true}", "reading": {"parent_value": 88, "unit": "DEGs", "evidence": "The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.", "target_result": "The paper reports that the analysis identified 88 differentially expressed genes.", "number_stated": true, "source_locator": "chars 1600-1686 of source sha256 c0dcbf60d04ef0239605a4f44d14bbf384886b7de824ce757251bcd342225a98"}, "recorded_at": "2026-10-31T15:18:37.408112+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "e2a54b8528cd10ab52e8a843794c4cc074f95f00336b2401c22c1218aab696ea", "source_hash": "c0dcbf60d04ef0239605a4f44d14bbf384886b7de824ce757251bcd342225a98", "raw_response": "<think>We need answer JSON only. Need identify single numerical result replication registered target headline numerical result main finding. Paper main finding: identified 88 DEGs and 27 central hub genes. User asks single numerical result headline number paper itself states for registered target \"the headline numerical result the paper states for its main finding\". Need decide 88 likely headline numerical result, perhaps 27 key genes? They demand single numerical result. Need parse language. Abstract: \"The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes... A group of 27 pivotal genes...\" Main headline perhaps 88 DEGs. Conclusion: \"we identified 88 DEGs and pinpointed 27 central hub genes\". Which is \"headline numerical result\" singular? Likely expected number 88, unit \"DEGs\". Evidence exact contiguous quote containing number. Could quote: \"The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.\" This directly attributes 88 to DEGs and exact quote. unit printed likely \"DEGs\". target_result maybe \"The analysis yielded 88 DEGs.\" Need JSON parent_value 88, unit \"DEGs\", evidence exact sentence. number_stated true.\n\nBut ambiguity: Main finding might be \"27 central hub genes\" due title key biomarkers and drug targets, registered target says headline numerical result paper states for its main finding. Need infer benchmark conventions. They likely ask extraction of a single numerical result from paper, perhaps target label generated from paper metadata? The source is likely abstract converted. The headline numerical result often \"88 DEGs\" because first result. Yet main finding could be 27 hub genes. Let's deeply assess.\n\nPrompt: \"Read the supplied paper text and find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed.\" Registered target: \"the headline numerical result the paper states for its main finding\". We need pick headline number. Abstract Results first sentence 88 DEGs. Then breakdown 66 and 22. \"A group of 27 pivotal genes\". Conclusion emphasizes \"identified 88 DEGs and pinpointed 27 central hub genes\". Paper's main finding can involve both. But asks single headline number likely 88 DEGs, because \"headline numerical result\" and unit. Maybe target is intentionally generic and need determine. Could perhaps select 27 as number of key genes identified, because title screening/identification key biomarkers/drug targets and final conclusion says \"Through our analysis, we identified 88 DEGs and pinpointed 27 central hub genes, which hold the potential to serve as diagnostic markers\". Which is headline? Both. Yet instruction says single. Usually in benchmark, registered target might be something like \"88 differentially expressed genes\" but they've paraphrased target vaguely? They explicitly label \"REGISTERED TARGET: the headline numerical result the paper states for its main finding.\" Maybe expected to identify most headline statistic. Need choose.\n\nLet's inspect source title \"Bioinformatics Analysis Screening and Identification of Key Biomarkers and Drug Targets in Human Glioblastoma\". Abstract likely from paper (Iranian Journal?). Typical abstract results: \"The analysis yielded 88 DEGs... A group of 27 pivotal genes was pinpointed...\" The headline numerical result may be 88 DEGs, perhaps because they ask a replication has to reproduce, registered target is \"the headline numerical result ...\". The first quantitative result is 88. Unit as printed \"DEGs\". Evidence must exact contiguous quote. If choose 88, evidence sentence.\n\nNeed output JSON object only. Ensure valid JSON, no markdown. target_result can explain \"The analysis yielded 88 DEGs.\" Or perhaps \"88 differentially expressed genes (DEGs).\" Unit must printed unit: \"DEGs\". The instruction \"Report the headline number only\" likely target_result should perhaps be concise. Could set target_result \"The paper reports 88 DEGs as the main analysis result.\" Evidence full clause. number_stated true.\n\nLet's ensure evidence exact contiguous source quote: \"The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.\" Yes exact. Unit \"DEGs\". parent_value 88. JSON.</think>\n\n{\"parent_value\":88,\"unit\":\"DEGs\",\"evidence\":\"The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.\",\"target_result\":\"The paper reports 88 differentially expressed genes as the headline result.\",\"number_stated\":true}", "reading": {"parent_value": 88, "unit": "DEGs", "evidence": "The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.", "target_result": "The paper reports 88 differentially expressed genes as the headline result.", "number_stated": true, "source_locator": "chars 1600-1686 of source sha256 c0dcbf60d04ef0239605a4f44d14bbf384886b7de824ce757251bcd342225a98"}, "recorded_at": "2026-10-31T15:18:29.102705+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes, and 27 pivotal hub genes were identified.", "minimax_alt": "The analysis yielded 88 differentially expressed genes (66 upregulated and 22 downregulated) and pinpointed 27 pivotal hub genes.", "decisive": false}, "analysis_methods": {"minimax": ["microarray analysis", "differentially expressed gene identification", "function enrichment analysis", "STRING protein-protein interaction network construction", "MCODE module analysis", "hub gene selection by connectivity degree", "hierarchical clustering", "Kaplan-Meier curve analyses"], "minimax_alt": ["Microarray analysis", "Differentially expressed gene (DEG) identification", "Function enrichment analysis", "Protein-protein interaction network construction using STRING version 10.0, with a combined interaction score greater than 0.4", "Molecular Complex Detection (MCODE) module analysis using Cytoscape version 3.4.0, with an MCODE score exceeding 5, degree cut-off of 2, node score cut-off of 0.2, maximum depth of 100, and k-score of 2", "DAVID functional enrichment analysis", "Hub-gene selection based on connectivity degrees of 10 or higher", "BiNGO biological-process analysis in Cytoscape", "Hierarchical clustering using the UCSC Cancer Genomics Browser"], "decisive": false}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "passed", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.passed"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:b6ae32827a9f340bbbc8e2537984988fa094fdc752770bbc21bf8d38621e2865", "type": "sep_package", "label": "SEP v1 package for pmid:39248068"}], "activities": [{"id": "activity:conversion:pmid:39248068", "type": "conversion", "used": ["package:b6ae32827a9f340bbbc8e2537984988fa094fdc752770bbc21bf8d38621e2865"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:39248068", "parent_hash": "sha256:7ee0a1f820ebfefa1c710ab9d229744e27b71b5e6b67ac1b200bb15dbb80622b", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39248068 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.passed", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:39248068' does not resolve to a declared asset", "targets"]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:45:43+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}}}