{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39739707", "kind": "science-record", "revision": 2, "content_hash": "sha256:e7860dac3ef158d9bea52d04b899d380545fb37f976d7509a9399ac7be051b52", "created_at": "2026-11-01T20:30:04Z", "updated_at": "2026-11-01T21:34:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "MiR-595 and Cldnd1: Potential related factors for bone loss in postmenopausal women with hip osteoporotic fracture.", "doi": "10.1371/journal.pone.0313106", "pmid": "39739707", "authors": ["Sun Jingyue", "Liu Peixin", "Wang Xiao"], "journal": "PloS one", "year": 2024, "abstract": "BACKGROUND: Recently researches have reported that miRNA and its target genes are associated with osteoporosis. MiRNA and mRNA might be potential diagnostic markers for osteoporosis.\nPURPOSES: The aim of this study is to explore the potential miRNA and mRNA markers by bioinformatics method and clinical analysis.\nPATIENTS AND METHODS: The miRNA expression profiles were obtained from GSE74209, GSE64433 and GSE115773 in Gene expression Omnibus (GEO). The mRNA expression profiles were obtained from GSE100609. Wayne intersection were used to explore the different expressed miRNAs (DE-miRs). Select the miRNA with the highest Fold Change for subsequent research. Screening of miRNA target genes using TargetScan and miRDB tools. GO and KEGG analyses of target genes (TGs) function were performed. Validate the selected TGs in the GSE100609. We collected female patients with femural intertrochanteric fractures from July 1, 2023 to October 31, 2023. Patient's bone marrow and clinical data were collected. MiRNA and the target mRNA differentially expressed in bone marrow were verified through RT-qPCR. All data were subjected to Shapiro-Wilk test. Using Pearson or Spearman test to detect the correlation between various indicators, and then incorporating indicators related to bone density into multiple linear regression equations. Partial correlation analysis was used to analyze the correlation between the final indicators and bone density.\nRESULTS: A total of 140 DE-miRs were identified. Set the fold change to \">1\" and ultimately include 5 miRNAs. Using miR-595 (highest |log2 FC|) as the subject of subsequent research. 3542 targeted mRNAs were predicted from TargetScan and 362 were from miRDB. 337 TGs were intersected, which were mainly enriched in nucleus. Only Cldnd1 were identified using the GSE100609 dataset. We found that miR-595 was highly expressed in patients with high bone mass, while Cldnd1 was downregulated. There was a strong collinearity between miR-595 and Cldnd1. Further multiple linear regression analysis showed a high correlation between miR-595 and bone density.\nCONCLUSIONS: These data suggest that miR-595 and Cldnd1 might be related factors for decreased bone mass.", "claims": [{"id": "claim-method", "statement": "Finally, partial correlation analysis was used to detect the correlation between miRNA and BMD.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39739707", "locator": "sections[10] \"Statistical analysis\" paragraph 2", "quote": "Finally, partial correlation analysis was used to detect the correlation between miRNA and BMD."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The relevant PMO datasets, GSE74209, GSE64433, GSE115773 and GSE100609, were downloaded from the GEO database (detailed information in S1–S4 Files). GSE74209, consists of miRNAs data corresponding to Homo sapiens, with 6 femoral neck trabecular bone obtained from postmenopausal women undergoing hip replacement due to osteoporotic fracture, and 6 form osteoarthritis in the absence of PMO.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39739707", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "The relevant PMO datasets, GSE74209, GSE64433, GSE115773 and GSE100609, were downloaded from the GEO database (detailed information in S1–S4 Files). GSE74209, consists of miRNAs data corresponding to Homo sapiens, with 6 femoral neck trabecular bone obtained from postmenopausal women undergoing hip replacement due to osteoporotic fracture, and 6 form osteoarthritis in the absence of PMO."}], "state": "complete"}, {"id": "claim-target-result", "statement": "After adjustment for age, miR-595 was strongly and positively correlated with bone mineral density, with a correlation coefficient of 0.953 (p<0.001).", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "The correlation coefficient was 0.953, p<0.001, indicating that miR-595 might be a related factor for BMD decline."}, "evidence": [{"asset": "source:pmid:39739707", "locator": "sections[15] \"Correlation analysis\" paragraph 2", "quote": "The correlation coefficient was 0.953, p<0.001, indicating that miR-595 might be a related factor for BMD decline."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "After adjustment for age, miR-595 was strongly and positively correlated with bone mineral density, with a correlation coefficient of 0.953 (p<0.001).", "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:39739707"], "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:GSE100609"], "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:GSE100609"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39739707", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0313106", "sha256": "sha256:b2a9df0a4a2aaaa55e65308cf5e3e169b2bec691d9f1c182641eeff944fd3889", "bytes": 26283, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0313106", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11687715", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100609", "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=GSE100609", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100609", "version": null, "note": "The relevant PMO datasets, GSE74209, GSE64433, GSE115773 and GSE100609, were downloaded from the GEO database (detailed information in S1–S4 Files). GSE74209, consists of miRNAs data corresponding to Homo sapiens, with 6 femoral neck trabecular bone obtained from postmenopausal women undergoing hip replacement due to osteoporotic fracture, and 6 form osteoarthritis in the absence of PMO.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The relevant PMO datasets, GSE74209, GSE64433, GSE115773 and GSE100609, were downloaded from the GEO database (detailed information in S1–S4 Files). GSE74209, consists of miRNAs data corresponding to Homo sapiens, with 6 femoral neck trabecular bone obtained from postmenopausal women undergoing hip replacement due to osteoporotic fracture, and 6 form osteoarthritis in the absence of PMO.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2688913", "GSM2688914", "GSM2688915", "GSM2688916", "GSM2688917", "GSM2688918", "GSM2688919", "GSM2688920"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "16699", "taxon": "Homo sapiens", "title": "Microarray profile of osteoporosis related genes of Indian post menopausal females", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE115773", "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=GSE115773", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE115773", "version": null, "note": "The relevant PMO datasets, GSE74209, GSE64433, GSE115773 and GSE100609, were downloaded from the GEO database (detailed information in S1–S4 Files). GSE74209, consists of miRNAs data corresponding to Homo sapiens, with 6 femoral neck trabecular bone obtained from postmenopausal women undergoing hip replacement due to osteoporotic fracture, and 6 form osteoarthritis in the absence of PMO.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The relevant PMO datasets, GSE74209, GSE64433, GSE115773 and GSE100609, were downloaded from the GEO database (detailed information in S1–S4 Files). GSE74209, consists of miRNAs data corresponding to Homo sapiens, with 6 femoral neck trabecular bone obtained from postmenopausal women undergoing hip replacement due to osteoporotic fracture, and 6 form osteoarthritis in the absence of PMO.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM3189518", "GSM3189519", "GSM3189520", "GSM3189521", "GSM3189522", "GSM3189523", "GSM3189524", "GSM3189525"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "22556", "taxon": "Homo sapiens", "title": "Real-time quantitative PCR analysis of serum from osteoporotic Mexican women", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE64433", "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=GSE64433", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE64433", "version": null, "note": "The relevant PMO datasets, GSE74209, GSE64433, GSE115773 and GSE100609, were downloaded from the GEO database (detailed information in S1–S4 Files). GSE74209, consists of miRNAs data corresponding to Homo sapiens, with 6 femoral neck trabecular bone obtained from postmenopausal women undergoing hip replacement due to osteoporotic fracture, and 6 form osteoarthritis in the absence of PMO.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The relevant PMO datasets, GSE74209, GSE64433, GSE115773 and GSE100609, were downloaded from the GEO database (detailed information in S1–S4 Files). GSE74209, consists of miRNAs data corresponding to Homo sapiens, with 6 femoral neck trabecular bone obtained from postmenopausal women undergoing hip replacement due to osteoporotic fracture, and 6 form osteoarthritis in the absence of PMO.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1571226", "GSM1571227", "GSM1571228", "GSM1571229", "GSM1571230", "GSM1571231"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "18402", "taxon": "Homo sapiens", "title": "Detection of potential microRNA biomarker for postmenopausal osteoporosis", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE74209", "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=GSE74209", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE74209", "version": null, "note": "The relevant PMO datasets, GSE74209, GSE64433, GSE115773 and GSE100609, were downloaded from the GEO database (detailed information in S1–S4 Files). GSE74209, consists of miRNAs data corresponding to Homo sapiens, with 6 femoral neck trabecular bone obtained from postmenopausal women undergoing hip replacement due to osteoporotic fracture, and 6 form osteoarthritis in the absence of PMO.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The relevant PMO datasets, GSE74209, GSE64433, GSE115773 and GSE100609, were downloaded from the GEO database (detailed information in S1–S4 Files). GSE74209, consists of miRNAs data corresponding to Homo sapiens, with 6 femoral neck trabecular bone obtained from postmenopausal women undergoing hip replacement due to osteoporotic fracture, and 6 form osteoarthritis in the absence of PMO.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1914622", "GSM1914623", "GSM1914624", "GSM1914625", "GSM1914626", "GSM1914627", "GSM1914628", "GSM1914629", "GSM1914630", "GSM1914631", "GSM1914632", "GSM1914633"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "20999", "taxon": "Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Betapolyomavirus hominis; Macacine alphaherpesvirus 1; Herpesvirus saimiri (strain 11); JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Merkel cell polyomavirus; Human alphaherpesvirus 2; Human betaherpesvirus 6B; human gammaherpesvirus 4; Betapolyomavirus macacae", "title": "MiRNA Profiling of Whole Trabecular Bone: Identification of Osteoporosis-Related Changes in MiRNAs in Human Hip Bones", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE100609 not downloaded", "asset:data:geo:GSE100609 licence not read", "asset:data:geo:GSE115773 not downloaded", "asset:data:geo:GSE115773 licence not read", "asset:data:geo:GSE64433 not downloaded", "asset:data:geo:GSE64433 licence not read", "asset:data:geo:GSE74209 not downloaded", "asset:data:geo:GSE74209 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Finally, partial correlation analysis was used to detect the correlation between miRNA and BMD."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "ols_fit", "expected_value": 0.001, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["ols_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ols."}, "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": ["GSE74209", "GSE64433", "GSE115773", "GSE100609"], "resolved_accessions": ["GSE74209", "GSE64433", "GSE115773", "GSE100609"], "statements": ["The relevant PMO datasets, GSE74209, GSE64433, GSE115773 and GSE100609, were downloaded from the GEO database (detailed information in S1–S4 Files). GSE74209, consists of miRNAs data corresponding to Homo sapiens, with 6 femoral neck trabecular bone obtained from postmenopausal women undergoing hip replacement due to osteoporotic fracture, and 6 form osteoarthritis in the absence of PMO."], "basis": "The paper names GSE74209, GSE64433, GSE115773, GSE100609 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": ["ols_fit"], "assets": ["source:pmid:39739707", "data:geo:GSE100609"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE100609"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:43:48Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 7745, "completion_tokens": 1935, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:39739707", "type": "paper", "label": "pmid:39739707"}, {"id": "source:pmid:39739707", "type": "manuscript", "label": "PMID 39739707 full text"}, {"id": "data:geo:GSE100609", "type": "dataset", "label": "GEO GSE100609"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39739707", "type": "paper", "label": "pmid:39739707"}, {"id": "source:pmid:39739707", "type": "manuscript", "label": "PMID 39739707 full text"}, {"id": "data:geo:GSE100609", "type": "dataset", "label": "GEO GSE100609"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39739707", "type": "extraction", "used": ["source:pmid:39739707"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE100609", "type": "accession_resolution", "used": ["data:geo:GSE100609"], "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:39739707", "parent_hash": "sha256:fdf66b073c58cb914d39fe137a057f55d581cbb13bd5265071f346eafca5ba60", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE100609 licence not read", "asset:data:geo:GSE100609 not downloaded", "asset:data:geo:GSE115773 licence not read", "asset:data:geo:GSE115773 not downloaded", "asset:data:geo:GSE64433 licence not read", "asset:data:geo:GSE64433 not downloaded", "asset:data:geo:GSE74209 licence not read", "asset:data:geo:GSE74209 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["pressed in bone marrow were verified through RT-qPCR. All data were subjected to Shapiro-Wilk tes", "ssed in bone marrow were verified through RT-qPCR. All data were subjected to Shapiro-Wilk tes"], "order_basis": "paper_text_order:1166", "id": "assay:1"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["ols_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Finally, partial correlation analysis was used to detect the correlation between miRNA and BMD."], "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":"2026-11-04T01:21:11+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}}}