{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32308427", "kind": "science-record", "revision": 8, "content_hash": "sha256:a083cbd87ea88ef348f2218ffbaa930f19fa96ef720583cdd245d4fc354f5410", "created_at": "2026-11-01T15:40:59Z", "updated_at": "2026-11-01T22:01:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of circRNA-miRNA-mRNA Networks for Exploring the Fundamental Mechanism in Lung Adenocarcinoma.", "doi": "10.2147/OTT.S235664", "pmid": "32308427", "authors": ["Liming Liang", "Liang Zhang", "Jiguang Zhang", "Shutang Bai", "Hongdu Fu"], "journal": "OncoTargets and therapy", "year": 2020, "abstract": "BACKGROUND: Circular RNAs (circRNAs) were elucidated to act as competing endogenous RNAs (ceRNAs) and to play significant roles in cancer initiation and progression. We aimed to identify the important circRNAs in lung adenocarcinoma and intended to predict the functions of them via the bioinformatics analysis.\nMETHODS: We extracted data from three Gene Expression Omnibus (GEO) datasets, GSE101586, GSE101684, and GSE104854, and identified the common differentially expressed circRNAs. Agarose gel electrophoresis and Sanger sequencing were used to verify these significant circRNAs. Then, qRT-PCR was performed to validate the expression through matched tissues and cell lines. Afterwards, a ceRNA network was constructed and functional analysis was performed to predict the potential mechanisms of circRNAs.\nRESULTS: Five circRNAs (hsa_circ_0072088, hsa_circ_0082564, hsa_circ_0008274, hsa_circ_0000519 and hsa_circ_0003528) were identified differentially expressed in the three datasets. Following the Agarose gel electrophoresis and qRT-PCR validation, hsa_circ_0072088 and hsa_circ_0008274 were chosen for further analysis. A ceRNA network of hsa_circ_0072088 and hsa_circ_0008274 was built based on the CSCD/TargetScan/MiRTarbase/StarBase 3.0. Then, the functional analysis showed that several meaningful terms were identified, such as \"epithelial to mesenchymal transition (EMT)\", \"Cellular response to TGF-β stimulus\", \"MAPK signaling pathway\", and \"PI3K-AKT signaling pathway\". Finally, several significant circRNA/miRNA/mRNA regulatory axes, which were predicted relating to cancer progress, were noted from the network.\nCONCLUSION: We identified significant circRNAs and meaningful circRNA-miRNA-mRNA networks to provide novel insight into pathogenesis and therapy of lung adenocarcinoma.", "claims": [{"id": "claim-data-access", "statement": "We downloaded raw data and re-organized them as raw counts expression matrix.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32308427", "locator": "sections[5] \"CircRNA Expression Profile Analysis\" paragraph 2", "quote": "We downloaded raw data and re-organized them as raw counts expression matrix."}], "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:32308427"], "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:GSE101586"], "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": {"fold_change": "in Table S2), plus, the fold-change and Student’s t testing"}, "inputs": ["data:geo:GSE101586"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32308427", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S235664", "sha256": "sha256:938c91380600a3520e5266f18137366345fa7e50df20b712ccc2f181a23222a0", "bytes": 21827, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/OTT.S235664", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7152915", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE101586", "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=GSE101586", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE101586", "version": null, "note": "We downloaded raw data and re-organized them as raw counts expression matrix.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded raw data and re-organized them as raw counts expression matrix.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2706423", "GSM2706424", "GSM2706425", "GSM2706426", "GSM2706427", "GSM2706428", "GSM2706429", "GSM2706430", "GSM2706431", "GSM2706432"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "19978", "taxon": "Homo sapiens", "title": "Profiling circular RNA expression in lung cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE101684", "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=GSE101684", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE101684", "version": null, "note": "We downloaded raw data and re-organized them as raw counts expression matrix.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded raw data and re-organized them as raw counts expression matrix.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2711988", "GSM2711989", "GSM2711990", "GSM2711991", "GSM2711992", "GSM2711993", "GSM2711994", "GSM2711995"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "21825", "taxon": "Homo sapiens", "title": "CircRNA expression profiles in early stage lung adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE104854", "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=GSE104854", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE104854", "version": null, "note": "We downloaded raw data and re-organized them as raw counts expression matrix.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded raw data and re-organized them as raw counts expression matrix.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2808849", "GSM2808850", "GSM2808851", "GSM2808852", "GSM2808853", "GSM2808854"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "17303", "taxon": "Homo sapiens", "title": "Ribosome-free RNA sequencing of long noncoding RNAs and circular RNAs in lung adenocarcinoma", "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:32308427:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a997898665662426f05c915166480451e985fa0b57ea947b94d8bc89358b14a3", "bytes": 635, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T0001", "version": null, "note": "Information of Expression Profiling Microarray Datasets", "structure": {"pmcid": "PMC7152915", "section_index": 5, "section_title": "CircRNA Expression Profile Analysis", "row_count": 5, "column_count": 7}, "table": {"label": "Table 1", "caption": "Information of Expression Profiling Microarray Datasets", "rows": [["Accession Number", "Platform", "Organism", "Experiment Type", "Status", "Numbers of Samples"], ["LAC", "Normal"], ["GSE101586", "GPL19978", "Homo sapiens", "Non-coding RNA profiling by array", "Public on Jul 19, 2017", "5", "5"], ["GSE101684", "GPL21825", "Homo sapiens", "Non-coding RNA profiling by array", "Public on Jun 26, 2019", "4", "4"], ["GSE104854", "GPL17303", "Homo sapiens", "Ribosome-free RNA sequencing", "Public on Oct 13, 2017", "3", "3"]], "row_count": 5, "column_count": 7, "numeric_cells": 15, "header_rows": 2, "locator": "section[5]/table-wrap[1]#T0001"}}, {"id": "asset:table:pmid:32308427:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:058e8f9cfd4ac055c63e47b0ae9eadca7b0acba273f49e4c9bc6c6ed97be94e2", "bytes": 568, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T0002", "version": null, "note": "Basic Information of Differentially Expressed circRNAs", "structure": {"pmcid": "PMC7152915", "section_index": 10, "section_title": "Identification of DECs", "row_count": 6, "column_count": 4}, "table": {"label": "Table 2", "caption": "Basic Information of Differentially Expressed circRNAs", "rows": [["CircRNA ID", "Position", "Spliced Length", "Gene Symbol"], ["hsa_circ_0072088", "chr5:32379220-32388780", "693", "ZFR"], ["hsa_circ_0082564", "chr7:137569740-137570248", "227", "CREB3L2"], ["hsa_circ_0008274", "chr13:96485180-96489456", "244", "UGGT2"], ["hsa_circ_0000519", "chr14:20811436-20811534", "98", "RPPH1"], ["hsa_circ_0003528", "chr5:134032815-134044578", "741", "SEC24A"]], "row_count": 6, "column_count": 4, "numeric_cells": 16, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T0002"}}, {"id": "asset:table:pmid:32308427:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6d6c970acae54ced5ce574088906c845fc63267066a0cc3d8a7671cde1ddc135", "bytes": 1079, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T0003", "version": null, "note": "Cancer-Related circRNA/miRNA/mRNA Axis", "structure": {"pmcid": "PMC7152915", "section_index": 14, "section_title": "Key circRNA-miRNA-mRNA Axis Analysis", "row_count": 10, "column_count": 4}, "table": {"label": "Table 3", "caption": "Cancer-Related circRNA/miRNA/mRNA Axis", "rows": [["circRNA", "miRNA", "mRNA", "Function Term"], ["has_circ_0072088", "miR-578", "ONECUT2/PRDM16/RPS27A/NEDD8/THBS1/COL1A1/ADAM9/PEG10/SIRT1/TGFB1/JUN/CREB1/TRIM33/WNT5A/CITED2", "Cellular response to TGF-β stimulus"], ["", "miR-578", "ONECUT2/PRDM16/RPS27A/NEDD8/THBS1/COL1A1/ADAM9/PEG10/SIRT1/TGFB1/JUN/CREB1/TRIM33/WNT5A/CITED2", "Response to TGF-β"], ["", "miR-944", "CACNG1/SRF/DDIT3/TRAF6/MAP4K2/TGFB1/JUN/FGFR2/FGF2/CACNG8", "MAPK signaling pathway"], ["", "miR-578", "SOD2/IGF1R/PIK3CA/PRKAA2/SIRT1/TGFB1/ATG12", "FoxO signaling pathway"], ["has_circ_0008274", "miR-578/miR-633", "WNT5A/TGFB1/HMGA2", "Epithelial to mesenchymal transition"], ["", "miR-578", "CREB1/GNB4/PRKAA2", "PI3K/AKT signaling pathway"], ["", "miR-578", "WNT5A/PRKAA2", "mTOR signaling pathway"], ["", "miR-633", "CACNG1/DDIT3/TRAF6/MAP4K2/TGFB1/JUN", "MAPK signaling pathway"], ["", "miR-633", "ATG12/SOD2/TGFB1/PRKAA2", "FoxO signaling pathway"]], "row_count": 10, "column_count": 4, "numeric_cells": 15, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T0003"}}], "gaps": ["asset:data:geo:GSE101586 not downloaded", "asset:data:geo:GSE101586 licence not read", "asset:data:geo:GSE101684 not downloaded", "asset:data:geo:GSE101684 licence not read", "asset:data:geo:GSE104854 not downloaded", "asset:data:geo:GSE104854 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fold_change": "in Table S2), plus, the fold-change and Student’s t testing"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-2", "family": null, "specific": null, "label": "Student’s t testing", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "“Then, limma R package was applied to normalize the raw counts (R code was provided in Table S2), plus, the fold-change and Student’s t testing were used for identifying differentially expressed circRNAs (DECs) in the two sets, respectively.”"}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE101586", "GSE101684", "GSE104854"], "resolved_accessions": ["GSE101586", "GSE101684", "GSE104854"], "statements": ["We downloaded raw data and re-organized them as raw counts expression matrix."], "basis": "The paper names GSE101586, GSE101684, GSE104854 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32308427", "data:geo:GSE101586", "asset:table:pmid:32308427:1", "asset:table:pmid:32308427:2", "asset:table:pmid:32308427:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE101586"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:19:26Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 17606, "completion_tokens": 1160, "cached_tokens": 776}}, "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:32308427", "type": "paper", "label": "pmid:32308427"}, {"id": "source:pmid:32308427", "type": "manuscript", "label": "PMID 32308427 full text"}, {"id": "data:geo:GSE101586", "type": "dataset", "label": "GEO GSE101586"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32308427", "type": "paper", "label": "pmid:32308427"}, {"id": "source:pmid:32308427", "type": "manuscript", "label": "PMID 32308427 full text"}, {"id": "data:geo:GSE101586", "type": "dataset", "label": "GEO GSE101586"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32308427", "type": "extraction", "used": ["source:pmid:32308427"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE101586", "type": "accession_resolution", "used": ["data:geo:GSE101586"], "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:32308427", "parent_hash": "sha256:008bc72a23e36dda1168fdba17085352f86b28de530ac6460dc78220ec7c75b4", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE101586 licence not read", "asset:data:geo:GSE101586 not downloaded", "asset:data:geo:GSE101684 licence not read", "asset:data:geo:GSE101684 not downloaded", "asset:data:geo:GSE104854 licence not read", "asset:data:geo:GSE104854 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["vine serum (FBS) and 1% antibiotics. All the cell lines were maintained at 37°C in a humidified atmosphere with 5% C", "e Academic of Science). The 16HBE cells were cultured in DMEM, and A549 and H1299 cells were cultured", "tured in DMEM, and A549 and H1299 cells were cultured in RPMI-1640 medium (Gibco, Invitrogen, Carlsba", "e Academic of Science). The 16HBE cells were cultured in DMEM, and A549 and H1299 cells were cultu"], "order_basis": "paper_text_order:1912", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["circRNA might play roles in tumor growth and apoptosis. Fewer cancer-related pathways were obtained"], "order_basis": "paper_text_order:3077", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["limma"], "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":"2026-11-04T02:43:43+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}}}