{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32127012", "kind": "science-record", "revision": 8, "content_hash": "sha256:764e608ec8aeaadf9738365dc83ce4d94c9b6f10dc93fd44edbcf6cfbc170a40", "created_at": "2026-11-01T15:40:57Z", "updated_at": "2026-11-01T22:44:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CDK1 and CDC20 overexpression in patients with colorectal cancer are associated with poor prognosis: evidence from integrated bioinformatics analysis.", "doi": "10.1186/s12957-020-01817-8", "pmid": "32127012", "authors": ["Jianxin Li", "Yinchun Wang", "Xin Wang", "Qingqiang Yang"], "journal": "World journal of surgical oncology", "year": 2020, "abstract": "BACKGROUND: Colorectal cancer (CRC) is one of the most common malignancies of the digestive system, which causes severe financial burden worldwide. However, the specific mechanisms involved in CRC are still unclear.\nMETHODS: To identify the significant genes and pathways involved in the initiation and progression of CRC, the microarray dataset GSE126092 was downloaded from Gene Expression Omnibus (GEO) database, and then, the data was analyzed to identify differentially expressed genes (DEGs). Subsequently, the Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed on these DEGs using the DAVID database, and the protein-protein interaction (PPI) network was constructed using the STRING database and analyzed using the Cytoscape software. Finally, hub genes were screened, and the survival analysis was performed on these hub genes using the Kaplan-Meier curves in the cBioPortal database.\nRESULTS: In total, 937 DEGs were obtained, including 316 upregulated genes and 621 downregulated genes. GO analysis revealed that the DEGs were mostly enriched in terms of nuclear division, organelle fission, cell division, and cell cycle process. KEGG pathway analysis showed that the DEGs were mostly enriched in cell cycle, oocyte meiosis, cytokine-cytokine receptor interaction, and cGMP-PKG signaling pathway. The PPI network comprised 608 nodes and 3100 edges, and 4 significant modules and 10 hub genes with the highest degree were identified using the Cytoscape software. Finally, survival analysis showed that overexpression of CDK1 and CDC20 in patients with CRC were statistically associated with worse overall survival.\nCONCLUSIONS: This bioinformatics analysis revealed that CDK1 and CDC20 might be candidate targets for diagnosis and treatment of CRC, which provided valuable clues for CRC.", "claims": [{"id": "claim-method", "statement": "In order to identify the potential prognostic role of these hub genes, the survival analysis of hub genes was performed using the Kaplan-Meier curves in the cBioPortal database (http://www.cbioportal.org) [16], and log rank test P value < 0.05 being the threshold of statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32127012", "locator": "sections[7] \"Survival analysis and validation of gene expression\" paragraph 2", "quote": "In order to identify the potential prognostic role of these hub genes, the survival analysis of hub genes was performed using the Kaplan-Meier curves in the cBioPortal database (http://www.cbioportal.org) [16], and log rank test P value < 0.05 being the threshold of statistical significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in the Gene Expression Omnibus (GEO) repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126092).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32127012", "locator": "sections[20] \"notes\" paragraph 1", "quote": "The datasets generated and/or analyzed during the current study are available in the Gene Expression Omnibus (GEO) repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126092)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32127012"], "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:GSE126092"], "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:GSE126092"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32127012", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12957-020-01817-8", "sha256": "sha256:b5632f780639e18838ad6ab49654a9e5575f90114129fce109173e0db8e243b2", "bytes": 32670, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12957-020-01817-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7055103", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE126092", "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=GSE126092", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE126092", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in the Gene Expression Omnibus (GEO) repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126092).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in the Gene Expression Omnibus (GEO) repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126092).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3591506", "GSM3591507", "GSM3591508", "GSM3591509", "GSM3591510", "GSM3591511", "GSM3591512", "GSM3591513", "GSM3591514", "GSM3591515", "GSM3591516", "GSM3591517", "GSM3591518", "GSM3591519", "GSM3591520", "GSM3591521", "GSM3591522", "GSM3591523", "GSM3591524", "GSM3591525"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "21047", "taxon": "Homo sapiens", "title": "Hsa_circ_101555 functions as a competing endogenous RNA of miR-597-5p to promote colorectal cancer progression [lncRNA/mRNAs]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32127012:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c19b6ad2ac01643d401776c09f5a7c928d4c06a56e60ead9f3a749a482d056e2", "bytes": 1990, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab2", "version": null, "note": "Functional roles of 10 hub genes", "structure": {"pmcid": "PMC7055103", "section_index": 6, "section_title": "Integration of protein-protein interaction network and module analysis", "row_count": 11, "column_count": 4}, "table": {"label": "Table 2", "caption": "Functional roles of 10 hub genes", "rows": [["No.", "Gene symbol", "Full name", "Function"], ["1", "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"], ["2", "CDC20", "Cell division cycle protein 20 homolog", "Required for full ubiquitin ligase activity of the anaphase promoting complex/cyclosome and may confer substrate specificity upon the complex"], ["3", "AURKA", "Aurora kinase A", "Mitotic serine/threonine kinase that contributes to the regulation of cell cycle progression."], ["4", "PLK1", "Polo-like kinase 1", "Serine/threonine-protein kinase that performs several important functions throughout M phase of the cell cycle"], ["5", "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"], ["6", "CDC6", "Cell division control protein 6 homolog", "Involved in the initiation of DNA replication. Also participates in checkpoint controls that ensure DNA replication is completed before mitosis is initiated"], ["7", "KIF11", "Kinesin family member 11", "Motor protein required for establishing a bipolar spindle during mitosis. Required in nonmitotic cells for transport of secretory proteins from the Golgi complex to the cell surface"], ["8", "CCNA2", "Cyclin A2", "Cyclin which controls both the G1/S and the G2/M transition phases of the cell cycle"], ["9", "CENPE", "Centromere-associated protein E", "Microtubule plus-end-directed kinetochore motor which plays an important role in chromosome congression, microtubule-kinetochore conjugation, and spindle assembly checkpoint activation"], ["10", "MKI67", "Marker of proliferation Ki-67", "Required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly"]], "row_count": 11, "column_count": 4, "numeric_cells": 19, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:32127012:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e5cd0d99b18ed07a7291db4f7a2b2ec5b4bf8906ba7d53bdeb08a1c109eaa038", "bytes": 3109, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab1", "version": null, "note": "Gene Ontology and KEGG pathway analysis of DEGs in colorectal cancer", "structure": {"pmcid": "PMC7055103", "section_index": 10, "section_title": "GO and KEGG enrichment analyses of DEGs", "row_count": 41, "column_count": 5}, "table": {"label": "Table 1", "caption": "Gene Ontology and KEGG pathway analysis of DEGs in colorectal cancer", "rows": [["Expression", "Category", "Term", "Count", "P value"], ["Upregulated", "GOTERM_BP_FAT", "GO:0000280~nuclear division", "40", "1.34E−18"], ["GOTERM_BP_FAT", "GO:0048285~organelle fission", "40", "1.23E−17"], ["GOTERM_BP_FAT", "GO:0051301~cell division", "37", "2.68E−16"], ["GOTERM_BP_FAT", "GO:0022402~cell cycle process", "56", "4.22E−16"], ["GOTERM_BP_FAT", "GO:0007049~cell cycle", "61", "3.43E−15"], ["GOTERM_CC_FAT", "GO:0005694~chromosome", "41", "1.95E−11"], ["GOTERM_CC_FAT", "GO:0000775~chromosome, centromeric region", "18", "4.41E−10"], ["GOTERM_CC_FAT", "GO:0005819~spindle", "22", "4.71E−10"], ["GOTERM_CC_FAT", "GO:0044427~chromosomal part", "36", "5.61E−10"], ["GOTERM_CC_FAT", "GO:0098687~chromosomal region", "22", "5.14E−09"], ["GOTERM_MF_FAT", "GO:0003777~microtubule motor activity", "10", "4.37E−07"], ["GOTERM_MF_FAT", "GO:0008009~chemokine activity", "7", "2.38E−05"], ["GOTERM_MF_FAT", "GO:0003774~motor activity", "10", "4.01E−05"], ["GOTERM_MF_FAT", "GO:0045236~CXCR chemokine receptor binding", "5", "4.08E−05"], ["GOTERM_MF_FAT", "GO:0005125~cytokine activity", "12", "7.12E−05"], ["KEGG_PATHWAY", "hsa04110:Cell cycle", "15", "9.41E−10"], ["KEGG_PATHWAY", "hsa04114:Oocyte meiosis", "10", "1.81E−05"], ["KEGG_PATHWAY", "hsa04914:Progesterone-mediated oocyte maturation", "9", "2.17E−05"], ["KEGG_PATHWAY", "hsa04060:Cytokine-cytokine receptor interaction", "13", "1.05E−04"], ["KEGG_PATHWAY", "hsa05322:Systemic lupus erythematosus", 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"identifier": "section[11]/table-wrap[1]#Tab2", "version": null, "note": "Functional roles of 10 hub genes", "structure": {"pmcid": "PMC7055103", "section_index": 11, "section_title": "Integration of protein-protein interaction network and module analysis", "row_count": 11, "column_count": 4}, "table": {"label": "Table 2", "caption": "Functional roles of 10 hub genes", "rows": [["No.", "Gene symbol", "Full name", "Function"], ["1", "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"], ["2", "CDC20", "Cell division cycle protein 20 homolog", "Required for full ubiquitin ligase activity of the anaphase promoting complex/cyclosome and may confer substrate specificity upon the complex"], ["3", "AURKA", "Aurora kinase A", "Mitotic serine/threonine kinase that contributes to the regulation of cell cycle progression."], ["4", "PLK1", "Polo-like kinase 1", "Serine/threonine-protein kinase that performs several important functions throughout M phase of the cell cycle"], ["5", "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"], ["6", "CDC6", "Cell division control protein 6 homolog", "Involved in the initiation of DNA replication. Also participates in checkpoint controls that ensure DNA replication is completed before mitosis is initiated"], ["7", "KIF11", "Kinesin family member 11", "Motor protein required for establishing a bipolar spindle during mitosis. Required in nonmitotic cells for transport of secretory proteins from the Golgi complex to the cell surface"], ["8", "CCNA2", "Cyclin A2", "Cyclin which controls both the G1/S and the G2/M transition phases of the cell cycle"], ["9", "CENPE", "Centromere-associated protein E", "Microtubule plus-end-directed kinetochore motor which plays an important role in chromosome congression, microtubule-kinetochore conjugation, and spindle assembly checkpoint activation"], ["10", "MKI67", "Marker of proliferation Ki-67", "Required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly"]], "row_count": 11, "column_count": 4, "numeric_cells": 19, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:GSE126092 not downloaded", "asset:data:geo:GSE126092 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In order to identify the potential prognostic role of these hub genes, the survival analysis of hub genes was performed using the Kaplan-Meier curves in the cBioPortal database (http://www.cbioportal.org) [16], and log rank test P value < 0.05 being the threshold of statistical significance."}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"p_value": "[16], and log rank test P value < 0"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log rank"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:32127012", "data:geo:GSE126092", "asset:table:pmid:32127012:1", "asset:table:pmid:32127012:2", "asset:table:pmid:32127012:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE126092"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:18:35Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 23764, "completion_tokens": 1532, "cached_tokens": 784}}, "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:32127012", "type": "paper", "label": "pmid:32127012"}, {"id": "source:pmid:32127012", "type": "manuscript", "label": "PMID 32127012 full text"}, {"id": "data:geo:GSE126092", "type": "dataset", "label": "GEO GSE126092"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32127012", "type": "paper", "label": "pmid:32127012"}, {"id": "source:pmid:32127012", "type": "manuscript", "label": "PMID 32127012 full text"}, {"id": "data:geo:GSE126092", "type": "dataset", "label": "GEO GSE126092"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32127012", "type": "extraction", "used": ["source:pmid:32127012"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE126092", "type": "accession_resolution", "used": ["data:geo:GSE126092"], "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:32127012", "parent_hash": "sha256:d7b015e6d06a4ead238f2fddb8a6d1d92fd9818d82f7bf9331450ea341ccde70", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE126092 licence not read", "asset:data:geo:GSE126092 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["n the initiation and progression of CRC, the microarray dataset GSE126092 was downloaded from Gene E"], "order_basis": "paper_text_order:433", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["In order to identify the potential prognostic role of these hub genes, the survival analysis of hub genes was performed using the Kaplan-Meier curves in the cBioPortal database (http://www.cbioportal.org) [16], and log rank test P value < 0.05 being the threshold of statistical significance."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T02:16:34+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}}}